Microbial strain improvement by a HTP genomic engineering platform

ABSTRACT

The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.

CROSS-REFERENCE TO RELATED APPLICATIONS

This Application is a Continuation Application of U.S. application Ser. No. 15/396,230, filed on Dec. 30, 2016, now issued as U.S. Pat. No. 9,988,624, which is a Continuation U.S. Utility Application under 35 U.S.C. § 111, which claiming the benefit of priority to International Application No. PCT/US2016/065465, filed on Dec. 7, 2016, which claims the benefit of priority to U.S. Provisional Application No. 62/264,232, filed on Dec. 7, 2015, U.S. Nonprovisional application Ser. No. 15/140,296, filed on Apr. 27, 2016, and U.S. Provisional Application No. 62/368,786, filed on Jul. 29, 2016, each of which are hereby incorporated by reference in their entirety, including all descriptions, references, figures, and claims for all purposes.

FIELD

The present disclosure is directed to high-throughput (HTP) microbial genomic engineering. The disclosed HTP genomic engineering platform is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition.

STATEMENT REGARDING SEQUENCE LISTING

The Sequence Listing associated with this application is provided in text format in lieu of a paper copy, and is hereby incorporated by reference into the specification. The name of the text file containing the Sequence Listing is ZYMR_001_04US_SeqList_ST25.txt. The text file is ≈5 KB, was created on Feb. 23, 2018, and is being submitted electronically via EFS-Web.

BACKGROUND

Humans have been harnessing the power of microbial cellular biosynthetic pathways for millennia to produce products of interest, the oldest examples of which include alcohol, vinegar, cheese, and yogurt. These products are still in large demand today and have also been accompanied by an ever increasing repertoire of products producible by microbes. The advent of genetic engineering technology has enabled scientists to design and program novel biosynthetic pathways into a variety of organisms to produce a broad range of industrial, medical, and consumer products. Indeed, microbial cellular cultures are now used to produce products ranging from small molecules, antibiotics, vaccines, insecticides, enzymes, fuels, and industrial chemicals.

Given the large number of products produced by modern industrial microbes, it comes as no surprise that engineers are under tremendous pressure to improve the speed and efficiency by which a given microorganism is able to produce a target product.

A variety of approaches have been used to improve the economy of biologically-based industrial processes by “improving” the microorganism involved. For example, many pharmaceutical and chemical industries rely on microbial strain improvement programs in which the parent strains of a microbial culture are continuously mutated through exposure to chemicals or UV radiation and are subsequently screened for performance increases, such as in productivity, yield and titer. This mutagenesis process is extensively repeated until a strain demonstrates a suitable increase in product performance. The subsequent “improved” strain is then utilized in commercial production.

As alluded to above, identification of improved industrial microbial strains through mutagenesis is time consuming and inefficient. The process, by its very nature, is haphazard and relies upon one stumbling upon a mutation that has a desirable outcome on product output.

Not only are traditional microbial strain improvement programs inefficient, but the process can also lead to industrial strains with a high degree of detrimental mutagenic load. The accumulation of mutations in industrial strains subjected to these types of programs can become significant and may lead to an eventual stagnation in the rate of performance improvement.

Thus, there is a great need in the art for new methods of engineering industrial microbes, which do not suffer from the aforementioned drawbacks inherent with traditional strain improvement programs and greatly accelerate the process of discovering and consolidating beneficial mutations.

Further, there is an urgent need for a method by which to “rehabilitate” industrial strains that have been developed by the antiquated and deleterious processes currently employed in the field of microbial strain improvement.

SUMMARY OF THE DISCLOSURE

The present disclosure provides a high-throughput (HTP) microbial genomic engineering platform that does not suffer from the myriad of problems associated with traditional microbial strain improvement programs.

Further, the HTP platform taught herein is able to rehabilitate industrial microbes that have accumulated non-beneficial mutations through decades of random mutagenesis-based strain improvement programs.

The disclosed HTP genomic engineering platform is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition.

The taught HTP genetic design libraries function as drivers of the genomic engineering process, by providing libraries of particular genomic alterations for testing in a microbe. The microbes engineered utilizing a particular library, or combination of libraries, are efficiently screened in a HTP manner for a resultant outcome, e.g. production of a product of interest. This process of utilizing the HTP genetic design libraries to define particular genomic alterations for testing in a microbe and then subsequently screening host microbial genomes harboring the alterations is implemented in an efficient and iterative manner. In some aspects, the iterative cycle or “rounds” of genomic engineering campaigns can be at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, or more iterations/cycles/rounds.

Thus, in some aspects, the present disclosure teaches methods of conducting at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675, 700, 725, 750, 775, 800, 825, 850, 875, 900, 925, 950, 975, 1000 or more “rounds” of HTP genetic engineering (e.g., rounds of SNP swap, PRO swap, STOP swap, or combinations thereof).

In some embodiments the present disclosure teaches a linear approach, in which each subsequent HTP genetic engineering round is based on genetic variation identified in the previous round of genetic engineering. In other embodiments the present disclosure teaches a non-linear approach, in which each subsequent HTP genetic engineering round is based on genetic variation identified in any previous round of genetic engineering, including previously conducted analysis, and separate HTP genetic engineering branches.

The data from these iterative cycles enables large scale data analytics and pattern recognition, which is utilized by the integrative platform to inform subsequent rounds of HTP genetic design library implementation. Consequently, the HTP genetic design libraries utilized in the taught platform are highly dynamic tools that benefit from large scale data pattern recognition algorithms and become more informative through each iterative round of microbial engineering.

In some embodiments, the genetic design libraries of the present disclosure comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675, 700, 725, 750, 775, 800, 825, 850, 875, 900, 925, 950, 975, 1000 or more individual genetic changes (e.g., at least X number of promoter:gene combinations in the PRO swap library).

In some embodiments, the present disclosure provides illustrative examples and text describing application of HTP strain improvement methods to microbial strains. In some embodiments, the strain improvement methods of the present disclosure are applicable to any host cell.

In some embodiments, the present disclosure teaches a high-throughput (HTP) method of genomic engineering to evolve a microbe to acquire a desired phenotype, comprising: a) perturbing the genomes of an initial plurality of microbes having the same microbial strain background, to thereby create an initial HTP genetic design microbial strain library comprising individual microbial strains with unique genetic variations; b) screening and selecting individual microbial strains of the initial HTP genetic design microbial strain library for the desired phenotype; c) providing a subsequent plurality of microbes that each comprise a unique combination of genetic variation, said genetic variation selected from the genetic variation present in at least two individual microbial strains screened in the preceding step, to thereby create a subsequent HTP genetic design microbial strain library; d) screening and selecting individual microbial strains of the subsequent HTP genetic design microbial strain library for the desired phenotype; e) repeating steps c)-d) one or more times, in a linear or non-linear fashion, until a microbe has acquired the desired phenotype, wherein each subsequent iteration creates a new HTP genetic design microbial strain library comprising individual microbial strains harboring unique genetic variations that are a combination of genetic variation selected from amongst at least two individual microbial strains of a preceding HTP genetic design microbial strain library.

In some embodiments, the present disclosure teaches that the initial HTP genetic design microbial strain library is at least one selected from the group consisting of a promoter swap microbial strain library, SNP swap microbial strain library, start/stop codon microbial strain library, optimized sequence microbial strain library, a terminator swap microbial strain library, or any combination thereof.

In some embodiments, the present disclosure teaches methods of making a subsequent plurality of microbes that each comprise a unique combination of genetic variations, wherein each of the combined genetic variations is derived from the initial HTP genetic design microbial strain library or the HTP genetic design microbial strain library of the preceding step.

In some embodiments, the combination of genetic variations in the subsequent plurality of microbes will comprise a subset of all the possible combinations of the genetic variations in the initial HTP genetic design microbial strain library or the HTP genetic design microbial strain library of the preceding step.

In some embodiments, the present disclosure teaches that the subsequent HTP genetic design microbial strain library is a full combinatorial microbial strain library derived from the genetic variations in the initial HTP genetic design microbial strain library or the HTP genetic design microbial strain library of the preceding step.

For example, if the prior HTP genetic design microbial strain library only had genetic variations A, B, C, and D, then a partial combinatorial of said variations could include a subsequent HTP genetic design microbial strain library comprising three microbes each comprising either the AB, AC, or AD unique combinations of genetic variations (order in which the mutations are represented is unimportant). A full combinatorial microbial strain library derived from the genetic variations of the HTP genetic design library of the preceding step would include six microbes, each comprising either AB, AC, AD, BC, BD, or CD unique combinations of genetic variations.

In some embodiments, the methods of the present disclosure teach perturbing the genome utilizing at least one method selected from the group consisting of: random mutagenesis, targeted sequence insertions, targeted sequence deletions, targeted sequence replacements, or any combination thereof.

In some embodiments of the presently disclosed methods, the initial plurality of microbes comprise unique genetic variations derived from an industrial production strain microbe.

In some embodiments of the presently disclosed methods, the initial plurality of microbes comprise industrial production strain microbes denoted S₁Gen₁ and any number of subsequent microbial generations derived therefrom denoted S_(n)Gen_(n).

In some embodiments, the present disclosure teaches a method for generating a SNP swap microbial strain library, comprising the steps of: a) providing a reference microbial strain and a second microbial strain, wherein the second microbial strain comprises a plurality of identified genetic variations selected from single nucleotide polymorphisms, DNA insertions, and DNA deletions, which are not present in the reference microbial strain; b) perturbing the genome of either the reference microbial strain, or the second microbial strain, to thereby create an initial SNP swap microbial strain library comprising a plurality of individual microbial strains with unique genetic variations found within each strain of said plurality of individual microbial strains, wherein each of said unique genetic variations corresponds to a single genetic variation selected from the plurality of identified genetic variations between the reference microbial strain and the second microbial strain.

In some embodiments of SNP swap library, the genome of the reference microbial strain is perturbed to add one or more of the identified single nucleotide polymorphisms, DNA insertions, or DNA deletions, which are found in the second microbial strain.

In some embodiments of SNP swap library methods of the present disclosure, the genome of the second microbial strain is perturbed to remove one or more of the identified single nucleotide polymorphisms, DNA insertions, or DNA deletions, which are not found in the reference microbial strain.

In some embodiments, the genetic variations of the SNP swap library will comprise a subset of all the genetic variations identified between the reference microbial strain and the second microbial strain.

In some embodiments, the genetic variations of the SNP swap library will comprise all of the identified genetic variations identified between the reference microbial strain and the second microbial strain.

In some embodiments, the present disclosure teaches a method for rehabilitating and improving the phenotypic performance of an industrial microbial strain, comprising the steps of: a) providing a parental lineage microbial strain and an industrial microbial strain derived therefrom, wherein the industrial microbial strain comprises a plurality of identified genetic variations selected from single nucleotide polymorphisms, DNA insertions, and DNA deletions, not present in the parental lineage microbial strain; b) perturbing the genome of either the parental lineage microbial strain, or the industrial microbial strain, to thereby create an initial SNP swap microbial strain library comprising a plurality of individual microbial strains with unique genetic variations found within each strain of said plurality of individual microbial strains, wherein each of said unique genetic variations corresponds to a single genetic variation selected from the plurality of identified genetic variations between the parental lineage microbial strain and the industrial microbial strain; c) screening and selecting individual microbial strains of the initial SNP swap microbial strain library for phenotype performance improvements over a reference microbial strain, thereby identifying unique genetic variations that confer said microbial strains with phenotype performance improvements; d) providing a subsequent plurality of microbes that each comprise a unique combination of genetic variation, said genetic variation selected from the genetic variation present in at least two individual microbial strains screened in the preceding step, to thereby create a subsequent SNP swap microbial strain library; e) screening and selecting individual microbial strains of the subsequent SNP swap microbial strain library for phenotype performance improvements over the reference microbial strain, thereby identifying unique combinations of genetic variation that confer said microbial strains with additional phenotype performance improvements; and f) repeating steps d)-e) one or more times, in a linear or non-linear fashion, until a microbial strain exhibits a desired level of improved phenotype performance compared to the phenotype performance of the industrial microbial strain, wherein each subsequent iteration creates a new SNP swap microbial strain library comprising individual microbial strains harboring unique genetic variations that are a combination of genetic variation selected from amongst at least two individual microbial strains of a preceding SNP swap microbial strain library.

In some embodiments the present disclosure teaches methods for rehabilitating and improving the phenotypic performance of an industrial microbial strain, wherein the genome of the parental lineage microbial strain is perturbed to add one or more of the identified single nucleotide polymorphisms, DNA insertions, or DNA deletions, which are found in the industrial microbial strain.

In some embodiments the present disclosure teaches methods for rehabilitating and improving the phenotypic performance of an industrial microbial strain, wherein the genome of the industrial microbial strain is perturbed to remove one or more of the identified single nucleotide polymorphisms, DNA insertions, or DNA deletions, which are not found in the parental lineage microbial strain.

In some embodiments, the present disclosure teaches a method for generating a promoter swap microbial strain library, said method comprising the steps of: a) providing a plurality of target genes endogenous to a base microbial strain, and a promoter ladder, wherein said promoter ladder comprises a plurality of promoters exhibiting different expression profiles in the base microbial strain; b) engineering the genome of the base microbial strain, to thereby create an initial promoter swap microbial strain library comprising a plurality of individual microbial strains with unique genetic variations found within each strain of said plurality of individual microbial strains, wherein each of said unique genetic variations comprises one of the promoters from the promoter ladder operably linked to one of the target genes endogenous to the base microbial strain.

In some embodiments, the present disclosure teaches a promoter swap method of genomic engineering to evolve a microbe to acquire a desired phenotype, said method comprising the steps of: a) providing a plurality of target genes endogenous to a base microbial strain, and a promoter ladder, wherein said promoter ladder comprises a plurality of promoters exhibiting different expression profiles in the base microbial strain; b) engineering the genome of the base microbial strain, to thereby create an initial promoter swap microbial strain library comprising a plurality of individual microbial strains with unique genetic variations found within each strain of said plurality of individual microbial strains, wherein each of said unique genetic variations comprises one of the promoters from the promoter ladder operably linked to one of the target genes endogenous to the base microbial strain; c) screening and selecting individual microbial strains of the initial promoter swap microbial strain library for the desired phenotype; d) providing a subsequent plurality of microbes that each comprise a unique combination of genetic variation, said genetic variation selected from the genetic variation present in at least two individual microbial strains screened in the preceding step, to thereby create a subsequent promoter swap microbial strain library; e) screening and selecting individual microbial strains of the subsequent promoter swap microbial strain library for the desired phenotype; f) repeating steps d)-e) one or more times, in a linear or non-linear fashion, until a microbe has acquired the desired phenotype, wherein each subsequent iteration creates a new promoter swap microbial strain library comprising individual microbial strains harboring unique genetic variations that are a combination of genetic variation selected from amongst at least two individual microbial strains of a preceding promoter swap microbial strain library.

In some embodiments, the present disclosure teaches a method for generating a terminator swap microbial strain library, said method comprising the steps of: a) providing a plurality of target genes endogenous to a base microbial strain, and a terminator ladder, wherein said terminator ladder comprises a plurality of terminators exhibiting different expression profiles in the base microbial strain; b) engineering the genome of the base microbial strain, to thereby create an initial terminator swap microbial strain library comprising a plurality of individual microbial strains with unique genetic variations found within each strain of said plurality of individual microbial strains, wherein each of said unique genetic variations comprises one of the target genes endogenous to the base microbial strain operably linked to one or more of the terminators from the terminator ladder.

In some embodiments, the present disclosure teaches a terminator swap method of genomic engineering to evolve a microbe to acquire a desired phenotype, said method comprising the steps of: a) providing a plurality of target genes endogenous to a base microbial strain, and a terminator ladder, wherein said terminator ladder comprises a plurality of terminators exhibiting different expression profiles in the base microbial strain; b) engineering the genome of the base microbial strain, to thereby create an initial terminator swap microbial strain library comprising a plurality of individual microbial strains with unique genetic variations found within each strain of said plurality of individual microbial strains, wherein each of said unique genetic variations comprises one of the target genes endogenous to the base microbial strain operably linked to one or more of the terminators from the terminator ladder; c) screening and selecting individual microbial strains of the initial terminator swap microbial strain library for the desired phenotype; d) providing a subsequent plurality of microbes that each comprise a unique combination of genetic variation, said genetic variation selected from the genetic variation present in at least two individual microbial strains screened in the preceding step, to thereby create a subsequent terminator swap microbial strain library; e) screening and selecting individual microbial strains of the subsequent terminator swap microbial strain library for the desired phenotype; f) repeating steps d)-e) one or more times, in a linear or non-linear fashion, until a microbe has acquired the desired phenotype, wherein each subsequent iteration creates a new terminator swap microbial strain library comprising individual microbial strains harboring unique genetic variations that are a combination of genetic variation selected from amongst at least two individual microbial strains of a preceding terminator swap microbial strain library.

In some embodiments, the present disclosure teaches iteratively improving the design of candidate microbial strains by (a) accessing a predictive model populated with a training set comprising (1) inputs representing genetic changes to one or more background microbial strains and (2) corresponding performance measures; (b) applying test inputs to the predictive model that represent genetic changes, the test inputs corresponding to candidate microbial strains incorporating those genetic changes; (c) predicting phenotypic performance of the candidate microbial strains based at least in part upon the predictive model; (d) selecting a first subset of the candidate microbial strains based at least in part upon their predicted performance; (e) obtaining measured phenotypic performance of the first subset of the candidate microbial strains; (f) obtaining a selection of a second subset of the candidate microbial strains based at least in part upon their measured phenotypic performance; (g) adding to the training set of the predictive model (1) inputs corresponding to the selected second subset of candidate microbial strains, along with (2) corresponding measured performance of the selected second subset of candidate microbial strains; and (h) repeating (b)-(g) until measured phenotypic performance of at least one candidate microbial strain satisfies a performance metric. In some cases, during a first application of test inputs to the predictive model, the genetic changes represented by the test inputs comprise genetic changes to the one or more background microbial strains; and during subsequent applications of test inputs, the genetic changes represented by the test inputs comprise genetic changes to candidate microbial strains within a previously selected second subset of candidate microbial strains.

In some embodiments, selection of the first subset may be based on epistatic effects. This may be achieved by: during a first selection of the first subset: determining degrees of dissimilarity between performance measures of the one or more background microbial strains in response to application of a plurality of respective inputs representing genetic changes to the one or more background microbial strains; and selecting for inclusion in the first subset at least two candidate microbial strains based at least in part upon the degrees of dissimilarity in the performance measures of the one or more background microbial strains in response to application of genetic changes incorporated into the at least two candidate microbial strains.

In some embodiments, the present invention teaches applying epistatic effects in the iterative improvement of candidate microbial strains, the method comprising: obtaining data representing measured performance in response to corresponding genetic changes made to at least one microbial background strain; obtaining a selection of at least two genetic changes based at least in part upon a degree of dissimilarity between the corresponding responsive performance measures of the at least two genetic changes, wherein the degree of dissimilarity relates to the degree to which the at least two genetic changes affect their corresponding responsive performance measures through different biological pathways; and designing genetic changes to a microbial background strain that include the selected genetic changes. In some cases, the microbial background strain for which the at least two selected genetic changes are designed is the same as the at least one microbial background strain for which data representing measured responsive performance was obtained.

In some embodiments, the present disclosure teaches HTP strain improvement methods utilizing only a single type of genetic microbial library. For example, in some embodiments, the present disclosure teaches HTP strain improvement methods utilizing only SNP swap libraries. In other embodiments, the present disclosure teaches HTP strain improvement methods utilizing only PRO swap libraries. In some embodiments, the present disclosure teaches HTP strain improvement methods utilizing only STOP swap libraries. In some embodiments, the present disclosure teaches HTP strain improvement methods utilizing only Start/Stop Codon swap libraries.

In other embodiments, the present disclosure teaches HTP strain improvement methods utilizing two or more types of genetic microbial libraries. For example, in some embodiments, the present disclosure teaches HTP strain improvement methods combining SNP swap and PRO swap libraries. In some embodiments, the present disclosure teaches HTP strain improvement methods combining SNP swap and STOP swap libraries. In some embodiments, the present disclosure teaches HTP strain improvement methods combining PRO swap and STOP swap libraries.

In other embodiments, the present disclosure teaches HTP strain improvement methods utilizing multiple types of genetic microbial libraries. In some embodiments the genetic microbial libraries are combined to produce combination mutations (e.g., promoter/terminator combination ladders applied to one or more genes). In yet other embodiments, the HTP strain improvement methods of the present disclosure can be combined with one or more traditional strain improvement methods.

In some embodiments, the HTP strain improvement methods of the present disclosure result in an improved host cell. That is, the present disclosure teaches methods of improving one or more host cell properties. In some embodiments the improved host cell property is selected from the group consisting of volumetric productivity, specific productivity, yield or titre, of a product of interest produced by the host cell. In some embodiments the improved host cell property is volumetric productivity. In some embodiments the improved host cell property is specific productivity. In some embodiments the improved host cell property is yield.

In some embodiments, the HTP strain improvement methods of the present disclosure result in a host cell that exhibits a 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 100%, 150%, 200%, 250%, 300% or more of an improvement in at least one host cell property over a control host cell that is not subjected to the HTP strain improvements methods (e.g, an X % improvement in yield or productivity of a biomolecule of interest, incorporating any ranges and subranges therebetween). In some embodiments, the HIT strain improvement methods of the present disclosure are selected from the group consisting of SNP swap, PRO swap, STOP swap, and combinations thereof.

Thus, in some embodiments, the SNP swap methods of the present disclosure result in a host cell that exhibits a 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 100%, 150%, 200%, 250%, 300% or more of an improvement in at least one host cell property over a control host cell that is not subjected to the SNP swap methods (e.g, an X % improvement in yield or productivity of a biomolecule of interest, incorporating any ranges and subranges therebetween).

Thus, in some embodiments, the PRO swap methods of the present disclosure result in a host cell that exhibits a 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 100%, 150%, 200%, 250%, 300% or more of an improvement in at least one host cell property over a control host cell that is not subjected to the PRO swap methods (e.g, an X % improvement in yield or productivity of a biomolecule of interest, incorporating any ranges and subranges therebetween).

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 depicts a DNA recombination method of the present disclosure for increasing variation in diversity pools. DNA sections, such as genome regions from related species, can be cut via physical or enzymatic/chemical means. The cut DNA regions are melted and allowed to reanneal, such that overlapping genetic regions prime polymerase extension reactions. Subsequent melting/extension reactions are carried out until products are reassembled into chimeric DNA, comprising elements from one or more starting sequences.

FIG. 2 outlines methods of the present disclosure for generating new host organisms with selected sequence modifications (e.g., 100 SNPs to swap). Briefly, the method comprises (1) desired DNA inserts are designed and generated by combining one or more synthesized oligos in an assembly reaction, (2) DNA inserts are cloned into transformation plasmids, (3) completed plasmids are transferred into desired production strains, where they are integrated into the host strain genome, and (4) selection markers and other unwanted DNA elements are looped out of the host strain. Each DNA assembly step may involve additional quality control (QC) steps, such as cloning plasmids into E. coli bacteria for amplification and sequencing.

FIG. 3 depicts assembly of transformation plasmids of the present disclosure, and their integration into host organisms. The insert DNA is generated by combining one or more synthesized oligos in an assembly reaction. DNA inserts containing the desired sequence are flanked by regions of DNA homologous to the targeted region of the genome. These homologous regions facilitate genomic integration, and, once integrated, form direct repeat regions designed for looping out vector backbone DNA in subsequent steps. Assembled plasmids contain the insert DNA, and optionally, one or more selection markers.

FIG. 4 depicts procedure for looping-out selected regions of DNA from host strains. Direct repeat regions of the inserted DNA and host genome can “loop out” in a recombination event. Cells counter selected for the selection marker contain deletions of the loop DNA flanked by the direct repeat regions.

FIG. 5 depicts an embodiment of the strain improvement process of the present disclosure. Host strain sequences containing genetic modifications (Genetic Design) are tested for strain performance improvements in various strain backgrounds (Strain Build). Strains exhibiting beneficial mutations are analyzed (Hit ID and Analysis) and the data is stored in libraries for further analysis (e.g., SNP swap libraries, PRO swap libraries, and combinations thereof, among others). Selection rules of the present disclosure generate new proposed host strain sequences based on the predicted effect of combining elements from one or more libraries for additional iterative analysis.

FIG. 6A-B depicts the DNA assembly, transformation, and strain screening steps of one of the embodiments of the present disclosure. FIG. 6A depicts the steps for building DNA fragments, cloning said DNA fragments into vectors, transforming said vectors into host strains, and looping out selection sequences through counter selection. FIG. 6B depicts the steps for high-throughput culturing, screening, and evaluation of selected host strains. This figure also depicts the optional steps of culturing, screening, and evaluating selected strains in culture tanks.

FIG. 7 depicts one embodiment of the automated system of the present disclosure. The present disclosure teaches use of automated robotic systems with various modules capable of cloning, transforming, culturing, screening and/or sequencing host organisms.

FIG. 8 depicts an overview of an embodiment of the host strain improvement program of the present disclosure.

FIG. 9 is a representation of the genome of Corynebacterium glutamicum, comprising around 3.2 million base pairs.

FIG. 10 depicts the results of a transformation experiment of the present disclosure. DNA inserts ranging from 0.5 kb to 5.0 kb were targeted for insertion into various regions (shown as relative positions 1-24) of the genome of Corynebacterium glutamicum. Light color indicates successful integration, while darker color indicates insertion failure.

FIG. 11 depicts the results of a second round HTP engineering PRO swap program. Top promoter::gene combinations identified during the first PRO swap round were analyzed according to the methods of the present disclosure to identify combinations of said mutations that would be likely to exhibit additive or combinatorial beneficial effects on host performance. Second round PRO swap mutants thus comprised pair combinations of various promoter::gene mutations. The resulting second round mutants were screened for differences in host cell yield of a selected biomolecule. A combination pair of mutations that had been predicted to exhibit beneficial effects is emphasized with a circle.

FIG. 12 depicts the results of an experiment testing successful plasmid assembly for plasmids transformed into E. coli. Picking four colonies is sufficient to achieve 13% failure rate for plasmids containing 1 and 2 kb insertion sequences. Larger insertions may require additional colony screening to achieve consistent results.

FIG. 13 depicts results of an experiment testing successful transformation of Corynebacterium glutamicum with insertion vectors. DNA insert sizes of 2 and 5 kb exhibited high transformation rates with low assembly failure rates.

FIG. 14 depicts results of loop out selections in Corynebacterium glutamicum. Sucrose resistance of transformed bacteria indicates loop out of sacB selection marker. DNA insert size does not appear to impact loop out efficiency.

FIG. 15 is a similarity matrix computed using the correlation measure. The matrix is a representation of the functional similarity between SNP variants. The consolidation of SNPs with low functional similarity is expected to have a higher likelihood of improving strain performance, as opposed to the consolidation of SNPs with higher functional similarity.

FIG. 16A-B depicts the results of an epistasis mapping experiment. Combination of SNPs and PRO swaps with low functional similarities yields improved strain performance. FIG. 16A depicts a dendrogram clustered by functional similarity of all the SNPs/PRO swaps. FIG. 16B depicts host strain performance of consolidated SNPs as measured by product yield. Greater cluster distance correlates with improved consolidation performance of the host strain.

FIG. 17A-B depicts SNP differences among strain variants in the diversity pool. FIG. 17A depicts the relationship among the strains of this experiment. Strain A is the wild-type host strain. Strain B is an intermediate engineered strain. Strain C is the industrial production strain. FIG. 17B is a graph identifying the number of unique and shared SNPs in each strain.

FIG. 18 depicts a first-round SNP swapping experiment according to the methods of the present disclosure. (1) all the SNPs from C will be individually and/or combinatorially cloned into the base A strain (“wave up” A to C). (2) all the SNPs from C will be individually and/or combinatorially removed from the commercial strain C (“wave down” C to A). (3) all the SNPs from B will be individually and/or combinatorially cloned into the base A strain (wave up A to B). (4) all the SNPs from B will be individually and/or combinatorially removed from the commercial strain B (wave down B to A). (5) all the SNPs unique to C will be individually and/or combinatorially cloned into the commercial B strain (wave up B to C). (6) all the SNPs unique to C will be individually and/or combinatorially removed from the commercial strain C (wave down C to B).

FIG. 19 illustrates example gene targets to be utilized in a promoter swap process.

FIG. 20 illustrates an exemplary promoter library that is being utilized to conduct a promoter swap process for the identified gene targets. Promoters utilized in the PRO swap (i.e. promoter swap) process are P₁-P₈, the sequences and identity of which can be found in Table 1.

FIG. 21 illustrates that promoter swapping genetic outcomes depend on the particular gene being targeted.

FIG. 22 depicts exemplary HTP promoter swapping data showing modifications that significantly affect performance on lysine yield. The X-axis represents different strains within the promoter swap genetic design microbial strain library, and the Y-axis includes relative lysine yield values for each strain. Each letter on the graph represents a PRO swap target gene. Each data point represents a replicate. The data demonstrates that a molecular tool adapted for HTP applications, as described herein (i.e. PRO swap), is able to efficiently create and optimize microbial strain performance for the production of a compound or molecule of interest. In this case, the compound of interest was lysine; however, the taught PRO swap molecular tool can be utilized to optimize and/or increase the production of any compound of interest. One of skill in the art would understand how to choose target genes, encoding the production of a desired compound, and then utilize the taught PRO swap procedure. One of skill in the art would readily appreciate that the demonstrated data exemplifying lysine yield increases taught herein, along with the detailed disclosure presented in the application, enables the PRO swap molecular tool to be a widely applicable advancement in HTP genomic engineering.

FIG. 23 illustrates the distribution of relative strain performances for the input data under consideration. A relative performance of zero indicates that the engineered strain performed equally well to the in-plate base strain. The processes described herein are designed to identify the strains that are likely to perform significantly above zero.

FIG. 24 illustrates the linear regression coefficient values, which depict the average change (increase or decrease) in relative strain performance associated with each genetic change incorporated into the depicted strains.

FIG. 25 illustrates the composition of changes for the top 100 predicted strain designs. The x-axis lists the pool of potential genetic changes (dss mutations are SNP swaps, and Pcg mutations are PRO swaps), and the y-axis shows the rank order. Black cells indicate the presence of a particular change in the candidate design, while white cells indicate the absence of that change. In this particular example, all of the top 100 designs contain the changes pcg3121_pgi, pcg1860_pyc, dss_339, and pcg0007_39_lysa. Additionally, the top candidate design contains the changes dss_034, dss_009.

FIG. 26 depicts the DNA assembly and transformation steps of one of the embodiments of the present disclosure. The flow chart depicts the steps for building DNA fragments, cloning said DNA fragments into vectors, transforming said vectors into host strains, and looping out selection sequences through counter selection.

FIG. 27 depicts the steps for high-throughput culturing, screening, and evaluation of selected host strains. This figure also depicts the optional steps of culturing, screening, and evaluating selected strains in culture tanks.

FIG. 28 depicts expression profiles of illustrative promoters exhibiting a range of regulatory expression, according to the promoter ladders of the present disclosure. Promoter A expression peaks at the lag phase of bacterial cultures, while promoter B and C peak at the exponential and stationary phase, respectively.

FIG. 29 depicts expression profiles of illustrative promoters exhibiting a range of regulatory expression, according to the promoter ladders of the present disclosure. Promoter A expression peaks immediately upon addition of a selected substrate, but quickly returns to undetectable levels as the concentration of the substrate is reduced. Promoter B expression peaks immediately upon addition of the selected substrate and lowers slowly back to undetectable levels together with the corresponding reduction in substrate. Promoter C expression peaks upon addition of the selected substrate, and remains highly expressed throughout the culture, even after the substrate has dissipated.

FIG. 30 depicts expression profiles of illustrative promoters exhibiting a range of constitutive expression levels, according to the promoter ladders of the present disclosure. Promoter A exhibits the lowest expression, followed by increasing expression levels promoter B and C, respectively.

FIG. 31 diagrams an embodiment of LIMS system of the present disclosure for strain improvement.

FIG. 32 diagrams a cloud computing implementation of embodiments of the LIMS system of the present disclosure.

FIG. 33 depicts an embodiment of the iterative predictive strain design workflow of the present disclosure.

FIG. 34 diagrams an embodiment of a computer system, according to embodiments of the present disclosure.

FIG. 35 depicts the workflow associated with the DNA assembly according to one embodiment of the present disclosure. This process is divided up into 4 stages: parts generation, plasmid assembly, plasmid QC, and plasmid preparation for transformation. During parts generation, oligos designed by Laboratory Information Management System (LIMS) are ordered from an oligo sequencing vendor and used to amplify the target sequences from the host organism via PCR. These PCR parts are cleaned to remove contaminants and assessed for success by fragment analysis, in silico quality control comparison of observed to theoretical fragment sizes, and DNA quantification. The parts are transformed into yeast along with an assembly vector and assembled into plasmids via homologous recombination. Assembled plasmids are isolated from yeast and transformed into E. coli for subsequent assembly quality control and amplification. During plasmid assembly quality control, several replicates of each plasmid are isolated, amplified using Rolling Circle Amplification (RCA), and assessed for correct assembly by enzymatic digest and fragment analysis. Correctly assembled plasmids identified during the QC process are hit picked to generate permanent stocks and the plasmid DNA extracted and quantified prior to transformation into the target host organism.

FIG. 36 depicts the results of an experiment characterizing the effects of Terminators T1-T8 in two media over two time points. Conditions A and C represent the two time points for the BHI media, while the B and D points represent the two time points for the HTP test media.

FIG. 37 depicts the results of an experiment comparing the effectiveness of traditional strain improvement approaches such as UV mutagenesis against the HTP engineering methodologies of the present disclosure. The vast majority of UV mutations produced no noticeable increase in host cell performance. In contrast, PRO swap methodologies of the present disclosure produced a high proportion of mutants exhibiting 1.2 to 2 fold increases in host cell performance.

FIG. 38 depicts the results of a first round HTP engineering SNP swap program. 186 individual SNP mutations were identified and individually cloned onto a base strain. The resulting mutants were screened for differences in host cell yield of a selected biomolecule.

FIG. 39 depicts the results of a second round HTP engineering SNP swap program. 176 individual SNP mutations from a first round SNP swap program were individually cloned into a second round host cell strain containing a beneficial SNP identified during a first round SNP program. The resulting mutants thus represent the effect of two mutation combination pairs. Screening results for differences in host cell yield (Y-axis) and productivity (X-axis) for the selected biomolecule are shown.

FIG. 40 depicts the results of a tank fermentation validation experiment. The top mutation pairs from the second round of HTP SNP swap were cultured in fermentation tanks. Results for host cell yield and productivity for the selected biomolecule (i.e. lysine) are shown. As can be seen, in one round of genomic engineering the inventors utilized the PRO swap procedure to determine that a particular PRO swap mutant (zwf) exhibited increased yield of a selected biomolecule compared to base strain (i.e. compare base strain to base strain+zwf). Then, the inventors performed another round of genomic engineering, wherein a SNP swap procedure was used to determine beneficial SNP mutations that could affect yield of the biomolecule, when combined with said PRO swap mutant. The combination of the PRO swap procedure and SNP swap procedure created mutants with even higher yields than the previous PRO swap only mutants (i.e. compare base strain+zwf+SNP121 to the previously discussed base strain+zwf). This figure illustrates the dramatic improvements in yield that can be achieved by combining the PRO swap and SNP swap procedures of the disclosure. In aspects, combining a PRO swap genomic engineering campaign with a SNP swap genomic engineering campaign can lead to increased yield and/or productivity of a biomolecule/product of interest by a factor of 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9% 10%, 15%, 20%, 25%, 30%, 40%, 45%, 50%, or more, relative to a base strain.

FIG. 41 depicts the results of a first round HTP engineering PRO swap program. Selected genes believed to be associated with host performance were combined with a promoter ladder to create a first round PRO swap library, according to the methods of the present disclosure. The resulting mutants were screened for differences in host cell yield of a selected biomolecule (i.e. lysine).

FIG. 42 is a flowchart illustrating the consideration of epistatic effects in the selection of mutations for the design of a microbial strain, according to embodiments of the disclosure.

FIG. 43A-B depicts the results of A. niger transformation and validation according to the methods of the present disclosure. FIG. 43A—is a picture of a 96-well media plate of A. niger transformants. Transformed cultures comprise a mutation in the aygA, which causes the cells to appear lighter yellow instead of black (transformed wells are circled in white). FIG. 43B—depicts the results of next generation sequencing of transformed A. niger mutants. The X-axis represents the target DNA's sequence identity with the untransformed parent strain. The Y-axis represents the target DNA's sequence identity with the expected mutation. Data points towards the bottom right of the chart exhibit high similarity with the parent strain, and low similarity with the expected transformed sequences. Data points towards the top left of the chart exhibit high similarity to expected transformed sequences and low identity with parent strain. Data points in the middle likely represent heterokaryons with multiple nuclei.

FIG. 44A-B illustrates a SNP swap implementation in A. Niger. FIG. 44A—illustrates the designed genetic edits for each SNP of the SNP swap. The figure further illustrates the cotransformation in which the pyrG gene is introduced into the locus for the aygA wild type gene. FIG. 44B—are two pictures of the 96-well media plates for screening the A. niger transformants. Light yellow colonies represent transformants in which the aygA gene has been successfully disrupted.

FIG. 45 depicts a quality control (QC) chart identifying successful A. niger mutant transformants (top box) based on next generation sequencing results. Overall 29.2% of yellow colonies selected from the culture plates exhibit the expected SNP genetic change.

FIG. 46 Depicts the results of next generation sequencing of transformed A. niger mutants. The X-axis represents the target DNA's sequence identity with the untransformed parent strain. The Y-axis represents the target DNA's sequence identity with the expected mutation. Data points towards the bottom right of the chart exhibit high similarity with the parent strain, and low similarity with the expected transformed sequences. Data points towards the top left of the chart exhibit high similarity to expected transformed sequences and low identity with parent strain. Data points in the middle likely represent heterokaryons with multiple nuclei.

FIG. 47 is a dot plot for the predicted performance vs measured performance of training data for a yield model of the present disclosure. The underlying model is a Kernel Ridge Regression model (with 4th order polynomial kernel). The model is trained on 1864 unique genetic constructs and associated phenotypic performance. The fitted model has an r2 value of 0.52.

FIG. 48 Depicts the genetic makeup of candidate designs generated by the prediction algorithms of the present disclosure. These candidate designs were submitted for HTP build and analysis. Here the candidate design is defined as the combination of parent strain id and introduced mutation(s).

FIG. 49 is a dot plot of the predicted performance vs. measured performance of candidate designs generated by the prediction algorithms of the present disclosure, and built according the HTP build methods of the present disclosure. This figure demonstrates that the model may predict candidate strain performance within an acceptable degree of accuracy.

FIG. 50 is a box and whiskers plot depicting the yield percent change of candidate strains with respect to parent strains. On the y-axis, a value of 0.01 corresponds to 1%. This figure demonstrates that strains designed by a computer model (light gray) achieve measureable improvement over their corresponding parent strains. Additionally, the figure demonstrates that these model base strain improvements are comparable in magnitude to improvements achieved by human expert designed strains.

FIG. 51 illustrates the yield performance distribution for strains designed by the computer model (dark grey) and by a human expert (light grey). Computer-designed strains exhibited tighter distributions with higher median gains.

FIG. 52 is a box and whiskers plot depicting the absolute yield of candidate strains generated by the computer (light grey) or by a human expert (dark grey). Results are aggregated by parent strain.

DETAILED DESCRIPTION Definitions

While the following terms are believed to be well understood by one of ordinary skill in the art, the following definitions are set forth to facilitate explanation of the presently disclosed subject matter.

The term “a” or “an” refers to one or more of that entity, i.e. can refer to a plural referents. As such, the terms “a” or “an”, “one or more” and “at least one” are used interchangeably herein. In addition, reference to “an element” by the indefinite article “a” or “an” does not exclude the possibility that more than one of the elements is present, unless the context clearly requires that there is one and only one of the elements.

As used herein the terms “cellular organism” “microorganism” or “microbe” should be taken broadly. These terms are used interchangeably and include, but are not limited to, the two prokaryotic domains, Bacteria and Archaea, as well as certain eukaryotic fungi and protists. In some embodiments, the disclosure refers to the “microorganisms” or “cellular organisms” or “microbes” of lists/tables and figures present in the disclosure. This characterization can refer to not only the identified taxonomic genera of the tables and figures, but also the identified taxonomic species, as well as the various novel and newly identified or designed strains of any organism in said tables or figures. The same characterization holds true for the recitation of these terms in other parts of the Specification, such as in the Examples.

The term “prokaryotes” is art recognized and refers to cells which contain no nucleus or other cell organelles. The prokaryotes are generally classified in one of two domains, the Bacteria and the Archaea. The definitive difference between organisms of the Archaea and Bacteria domains is based on fundamental differences in the nucleotide base sequence in the 16S ribosomal RNA.

The term “Archaea” refers to a categorization of organisms of the division Mendosicutes, typically found in unusual environments and distinguished from the rest of the prokaryotes by several criteria, including the number of ribosomal proteins and the lack of muramic acid in cell walls. On the basis of ssrRNA analysis, the Archaea consist of two phylogenetically-distinct groups: Crenarchaeota and Euryarchaeota. On the basis of their physiology, the Archaea can be organized into three types: methanogens (prokaryotes that produce methane); extreme halophiles (prokaryotes that live at very high concentrations of salt (NaCl); and extreme (hyper) thermophilus (prokaryotes that live at very high temperatures). Besides the unifying archaeal features that distinguish them from Bacteria (i.e., no murein in cell wall, ester-linked membrane lipids, etc.), these prokaryotes exhibit unique structural or biochemical attributes which adapt them to their particular habitats. The Crenarchaeota consists mainly of hyperthermophilic sulfur-dependent prokaryotes and the Euryarchaeota contains the methanogens and extreme halophiles.

“Bacteria” or “eubacteria” refers to a domain of prokaryotic organisms. Bacteria include at least 11 distinct groups as follows: (1) Gram-positive (gram+) bacteria, of which there are two major subdivisions: (1) high G+C group (Actinomycetes, Mycobacteria, Micrococcus, others) (2) low G+C group (Bacillus, Clostridia, Lactobacillus, Staphylococci, Streptococci, Mycoplasmas); (2) Proteobacteria, e.g., Purple photosynthetic+non-photosynthetic Gram-negative bacteria (includes most “common” Gram-negative bacteria); (3) Cyanobacteria, e.g., oxygenic phototrophs; (4) Spirochetes and related species; (5) Planctomyces; (6) Bacteroides, Flavobacteria; (7) Chlamydia; (8) Green sulfur bacteria; (9) Green non-sulfur bacteria (also anaerobic phototrophs); (10) Radioresistant micrococci and relatives; (11) Thermotoga and Thermosipho thermophiles.

A “eukaryote” is any organism whose cells contain a nucleus and other organelles enclosed within membranes. Eukaryotes belong to the taxon Eukarya or Eukaryota. The defining feature that sets eukaryotic cells apart from prokaryotic cells (the aforementioned Bacteria and Archaea) is that they have membrane-bound organelles, especially the nucleus, which contains the genetic material, and is enclosed by the nuclear envelope.

The terms “genetically modified host cell,” “recombinant host cell,” and “recombinant strain” are used interchangeably herein and refer to host cells that have been genetically modified by the cloning and transformation methods of the present disclosure. Thus, the terms include a host cell (e.g., bacteria, yeast cell, fungal cell, CHO, human cell, etc.) that has been genetically altered, modified, or engineered, such that it exhibits an altered, modified, or different genotype and/or phenotype (e.g., when the genetic modification affects coding nucleic acid sequences of the microorganism), as compared to the naturally-occurring organism from which it was derived. It is understood that in some embodiments, the terms refer not only to the particular recombinant host cell in question, but also to the progeny or potential progeny of such a host cell

The term “wild-type microorganism” or “wild-type host cell” describes a cell that occurs in nature, i.e. a cell that has not been genetically modified.

The term “genetically engineered” may refer to any manipulation of a host cell's genome (e.g. by insertion, deletion, mutation, or replacement of nucleic acids).

The term “control” or “control host cell” refers to an appropriate comparator host cell for determining the effect of a genetic modification or experimental treatment. In some embodiments, the control host cell is a wild type cell. In other embodiments, a control host cell is genetically identical to the genetically modified host cell, save for the genetic modification(s) differentiating the treatment host cell. In some embodiments, the present disclosure teaches the use of parent strains as control host cells (e.g., the S₁ strain that was used as the basis for the strain improvement program). In other embodiments, a host cell may be a genetically identical cell that lacks a specific promoter or SNP being tested in the treatment host cell.

As used herein, the term “allele(s)” means any of one or more alternative forms of a gene, all of which alleles relate to at least one trait or characteristic. In a diploid cell, the two alleles of a given gene occupy corresponding loci on a pair of homologous chromosomes.

As used herein, the term “locus” (loci plural) means a specific place or places or a site on a chromosome where for example a gene or genetic marker is found.

As used herein, the term “genetically linked” refers to two or more traits that are co-inherited at a high rate during breeding such that they are difficult to separate through crossing.

A “recombination” or “recombination event” as used herein refers to a chromosomal crossing over or independent assortment.

As used herein, the term “phenotype” refers to the observable characteristics of an individual cell, cell culture, organism, or group of organisms which results from the interaction between that individual's genetic makeup (i.e., genotype) and the environment.

As used herein, the term “chimeric” or “recombinant” when describing a nucleic acid sequence or a protein sequence refers to a nucleic acid, or a protein sequence, that links at least two heterologous polynucleotides, or two heterologous polypeptides, into a single macromolecule, or that re-arranges one or more elements of at least one natural nucleic acid or protein sequence. For example, the term “recombinant” can refer to an artificial combination of two otherwise separated segments of sequence, e.g., by chemical synthesis or by the manipulation of isolated segments of nucleic acids by genetic engineering techniques.

As used herein, a “synthetic nucleotide sequence” or “synthetic polynucleotide sequence” is a nucleotide sequence that is not known to occur in nature or that is not naturally occurring. Generally, such a synthetic nucleotide sequence will comprise at least one nucleotide difference when compared to any other naturally occurring nucleotide sequence.

As used herein, the term “nucleic acid” refers to a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides, or analogs thereof. This term refers to the primary structure of the molecule, and thus includes double- and single-stranded DNA, as well as double- and single-stranded RNA. It also includes modified nucleic acids such as methylated and/or capped nucleic acids, nucleic acids containing modified bases, backbone modifications, and the like. The terms “nucleic acid” and “nucleotide sequence” are used interchangeably.

As used herein, the term “gene” refers to any segment of DNA associated with a biological function. Thus, genes include, but are not limited to, coding sequences and/or the regulatory sequences required for their expression. Genes can also include non-expressed DNA segments that, for example, form recognition sequences for other proteins. Genes can be obtained from a variety of sources, including cloning from a source of interest or synthesizing from known or predicted sequence information, and may include sequences designed to have desired parameters.

As used herein, the term “homologous” or “homologue” or “ortholog” is known in the art and refers to related sequences that share a common ancestor or family member and are determined based on the degree of sequence identity. The terms “homology,” “homologous,” “substantially similar” and “corresponding substantially” are used interchangeably herein. They refer to nucleic acid fragments wherein changes in one or more nucleotide bases do not affect the ability of the nucleic acid fragment to mediate gene expression or produce a certain phenotype. These terms also refer to modifications of the nucleic acid fragments of the instant disclosure such as deletion or insertion of one or more nucleotides that do not substantially alter the functional properties of the resulting nucleic acid fragment relative to the initial, unmodified fragment. It is therefore understood, as those skilled in the art will appreciate, that the disclosure encompasses more than the specific exemplary sequences. These terms describe the relationship between a gene found in one species, subspecies, variety, cultivar or strain and the corresponding or equivalent gene in another species, subspecies, variety, cultivar or strain. For purposes of this disclosure homologous sequences are compared. “Homologous sequences” or “homologues” or “orthologs” are thought, believed, or known to be functionally related. A functional relationship may be indicated in any one of a number of ways, including, but not limited to: (a) degree of sequence identity and/or (b) the same or similar biological function. Preferably, both (a) and (b) are indicated. Homology can be determined using software programs readily available in the art, such as those discussed in Current Protocols in Molecular Biology (F. M. Ausubel et al., eds., 1987) Supplement 30, section 7.718, Table 7.71. Some alignment programs are MacVector (Oxford Molecular Ltd, Oxford, U.K.), ALIGN Plus (Scientific and Educational Software, Pennsylvania) and AlignX (Vector NTI, Invitrogen, Carlsbad, Calif.). Another alignment program is Sequencher (Gene Codes, Ann Arbor, Mich.), using default parameters.

As used herein, the term “endogenous” or “endogenous gene,” refers to the naturally occurring gene, in the location in which it is naturally found within the host cell genome. In the context of the present disclosure, operably linking a heterologous promoter to an endogenous gene means genetically inserting a heterologous promoter sequence in front of an existing gene, in the location where that gene is naturally present. An endogenous gene as described herein can include alleles of naturally occurring genes that have been mutated according to any of the methods of the present disclosure.

As used herein, the term “exogenous” is used interchangeably with the term “heterologous,” and refers to a substance coming from some source other than its native source. For example, the terms “exogenous protein,” or “exogenous gene” refer to a protein or gene from a non-native source or location, and that have been artificially supplied to a biological system.

As used herein, the term “nucleotide change” refers to, e.g., nucleotide substitution, deletion, and/or insertion, as is well understood in the art. For example, mutations contain alterations that produce silent substitutions, additions, or deletions, but do not alter the properties or activities of the encoded protein or how the proteins are made.

As used herein, the term “protein modification” refers to, e.g., amino acid substitution, amino acid modification, deletion, and/or insertion, as is well understood in the art.

As used herein, the term “at least a portion” or “fragment” of a nucleic acid or polypeptide means a portion having the minimal size characteristics of such sequences, or any larger fragment of the full length molecule, up to and including the full length molecule. A fragment of a polynucleotide of the disclosure may encode a biologically active portion of a genetic regulatory element. A biologically active portion of a genetic regulatory element can be prepared by isolating a portion of one of the polynucleotides of the disclosure that comprises the genetic regulatory element and assessing activity as described herein. Similarly, a portion of a polypeptide may be 4 amino acids, 5 amino acids, 6 amino acids, 7 amino acids, and so on, going up to the full length polypeptide. The length of the portion to be used will depend on the particular application. A portion of a nucleic acid useful as a hybridization probe may be as short as 12 nucleotides; in some embodiments, it is 20 nucleotides. A portion of a polypeptide useful as an epitope may be as short as 4 amino acids. A portion of a polypeptide that performs the function of the full-length polypeptide would generally be longer than 4 amino acids.

Variant polynucleotides also encompass sequences derived from a mutagenic and recombinogenic procedure such as DNA shuffling. Strategies for such DNA shuffling are known in the art. See, for example, Stemmer (1994) PNAS 91:10747-10751; Stemmer (1994) Nature 370:389-391; Crameri et al. (1997) Nature Biotech. 15:436-438; Moore et al. (1997) J. Mol. Biol. 272:336-347; Zhang et al. (1997) PNAS 94:4504-4509; Crameri et al. (1998) Nature 391:288-291; and U.S. Pat. Nos. 5,605,793 and 5,837,458.

For PCR amplifications of the polynucleotides disclosed herein, oligonucleotide primers can be designed for use in PCR reactions to amplify corresponding DNA sequences from cDNA or genomic DNA extracted from any organism of interest. Methods for designing PCR primers and PCR cloning are generally known in the art and are disclosed in Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual (3^(rd) ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.). See also Innis et al., eds. (1990) PCR Protocols: A Guide to Methods and Applications (Academic Press, New York); Innis and Gelfand, eds. (1995) PCR Strategies (Academic Press, New York); and Innis and Gelfand, eds. (1999) PCR Methods Manual (Academic Press, New York). Known methods of PCR include, but are not limited to, methods using paired primers, nested primers, single specific primers, degenerate primers, gene-specific primers, vector-specific primers, partially-mismatched primers, and the like.

The term “primer” as used herein refers to an oligonucleotide which is capable of annealing to the amplification target allowing a DNA polymerase to attach, thereby serving as a point of initiation of DNA synthesis when placed under conditions in which synthesis of primer extension product is induced, i.e., in the presence of nucleotides and an agent for polymerization such as DNA polymerase and at a suitable temperature and pH. The (amplification) primer is preferably single stranded for maximum efficiency in amplification. Preferably, the primer is an oligodeoxyribonucleotide. The primer must be sufficiently long to prime the synthesis of extension products in the presence of the agent for polymerization. The exact lengths of the primers will depend on many factors, including temperature and composition (A/T vs. G/C content) of primer. A pair of bi-directional primers consists of one forward and one reverse primer as commonly used in the art of DNA amplification such as in PCR amplification.

As used herein, “promoter” refers to a DNA sequence capable of controlling the expression of a coding sequence or functional RNA. In some embodiments, the promoter sequence consists of proximal and more distal upstream elements, the latter elements often referred to as enhancers. Accordingly, an “enhancer” is a DNA sequence that can stimulate promoter activity, and may be an innate element of the promoter or a heterologous element inserted to enhance the level or tissue specificity of a promoter. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental conditions. It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, DNA fragments of some variation may have identical promoter activity.

As used herein, the phrases “recombinant construct”, “expression construct”, “chimeric construct”, “construct”, and “recombinant DNA construct” are used interchangeably herein. A recombinant construct comprises an artificial combination of nucleic acid fragments, e.g., regulatory and coding sequences that are not found together in nature. For example, a chimeric construct may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. Such construct may be used by itself or may be used in conjunction with a vector. If a vector is used then the choice of vector is dependent upon the method that will be used to transform host cells as is well known to those skilled in the art. For example, a plasmid vector can be used. The skilled artisan is well aware of the genetic elements that must be present on the vector in order to successfully transform, select and propagate host cells comprising any of the isolated nucleic acid fragments of the disclosure. The skilled artisan will also recognize that different independent transformation events will result in different levels and patterns of expression (Jones et al., (1985) EMBO J. 4:2411-2418; De Almeida et al., (1989) Mol. Gen. Genetics 218:78-86), and thus that multiple events must be screened in order to obtain lines displaying the desired expression level and pattern. Such screening may be accomplished by Southern analysis of DNA, Northern analysis of mRNA expression, immunoblotting analysis of protein expression, or phenotypic analysis, among others. Vectors can be plasmids, viruses, bacteriophages, pro-viruses, phagemids, transposons, artificial chromosomes, and the like, that replicate autonomously or can integrate into a chromosome of a host cell. A vector can also be a naked RNA polynucleotide, a naked DNA polynucleotide, a polynucleotide composed of both DNA and RNA within the same strand, a poly-lysine-conjugated DNA or RNA, a peptide-conjugated DNA or RNA, a liposome-conjugated DNA, or the like, that is not autonomously replicating. As used herein, the term “expression” refers to the production of a functional end-product e.g., an mRNA or a protein (precursor or mature).

“Operably linked” means in this context the sequential arrangement of the promoter polynucleotide according to the disclosure with a further oligo- or polynucleotide, resulting in transcription of said further polynucleotide.

The term “product of interest” or “biomolecule” as used herein refers to any product produced by microbes from feedstock. In some cases, the product of interest may be a small molecule, enzyme, peptide, amino acid, organic acid, synthetic compound, fuel, alcohol, etc. For example, the product of interest or biomolecule may be any primary or secondary extracellular metabolite. The primary metabolite may be, inter alia, ethanol, citric acid, lactic acid, glutamic acid, glutamate, lysine, threonine, tryptophan and other amino acids, vitamins, polysaccharides, etc. The secondary metabolite may be, inter alia, an antibiotic compound like penicillin, or an immunosuppressant like cyclosporin A, a plant hormone like gibberellin, a statin drug like lovastatin, a fungicide like griseofulvin, etc. The product of interest or biomolecule may also be any intracellular component produced by a microbe, such as: a microbial enzyme, including: catalase, amylase, protease, pectinase, glucose isomerase, cellulase, hemicellulase, lipase, lactase, streptokinase, and many others. The intracellular component may also include recombinant proteins, such as: insulin, hepatitis B vaccine, interferon, granulocyte colony-stimulating factor, streptokinase and others.

The term “carbon source” generally refers to a substance suitable to be used as a source of carbon for cell growth. Carbon sources include, but are not limited to, biomass hydrolysates, starch, sucrose, cellulose, hemicellulose, xylose, and lignin, as well as monomeric components of these substrates. Carbon sources can comprise various organic compounds in various forms, including, but not limited to polymers, carbohydrates, acids, alcohols, aldehydes, ketones, amino acids, peptides, etc. These include, for example, various monosaccharides such as glucose, dextrose (D-glucose), maltose, oligosaccharides, polysaccharides, saturated or unsaturated fatty acids, succinate, lactate, acetate, ethanol, etc., or mixtures thereof. Photosynthetic organisms can additionally produce a carbon source as a product of photosynthesis. In some embodiments, carbon sources may be selected from biomass hydrolysates and glucose.

The term “feedstock” is defined as a raw material or mixture of raw materials supplied to a microorganism or fermentation process from which other products can be made. For example, a carbon source, such as biomass or the carbon compounds derived from biomass are a feedstock for a microorganism that produces a product of interest (e.g. small molecule, peptide, synthetic compound, fuel, alcohol, etc.) in a fermentation process. However, a feedstock may contain nutrients other than a carbon source.

The term “volumetric productivity” or “production rate” is defined as the amount of product formed per volume of medium per unit of time. Volumetric productivity can be reported in gram per liter per hour (g/L/h).

The term “specific productivity” is defined as the rate of formation of the product. Specific productivity is herein further defined as the specific productivity in gram product per gram of cell dry weight (CDW) per hour (g/g CDW/h). Using the relation of CDW to OD₆₀₀ for the given microorganism specific productivity can also be expressed as gram product per liter culture medium per optical density of the culture broth at 600 nm (OD) per hour (g/L/h/OD).

The term “yield” is defined as the amount of product obtained per unit weight of raw material and may be expressed as g product per g substrate (g/g). Yield may be expressed as a percentage of the theoretical yield. “Theoretical yield” is defined as the maximum amount of product that can be generated per a given amount of substrate as dictated by the stoichiometry of the metabolic pathway used to make the product.

The term “titre” or “titer” is defined as the strength of a solution or the concentration of a substance in solution. For example, the titre of a product of interest (e.g. small molecule, peptide, synthetic compound, fuel, alcohol, etc.) in a fermentation broth is described as g of product of interest in solution per liter of fermentation broth (g/L).

The term “total titer” is defined as the sum of all product of interest produced in a process, including but not limited to the product of interest in solution, the product of interest in gas phase if applicable, and any product of interest removed from the process and recovered relative to the initial volume in the process or the operating volume in the process

As used herein, the term “HTP genetic design library” or “library” refers to collections of genetic perturbations according to the present disclosure. In some embodiments, the libraries of the present invention may manifest as i) a collection of sequence information in a database or other computer file, ii) a collection of genetic constructs encoding for the aforementioned series of genetic elements, or iii) host cell strains comprising said genetic elements. In some embodiments, the libraries of the present disclosure may refer to collections of individual elements (e.g., collections of promoters for PRO swap libraries, or collections of terminators for STOP swap libraries). In other embodiments, the libraries of the present disclosure may also refer to combinations of genetic elements, such as combinations of promoter::genes, gene:terminator, or even promoter:gene:terminators. In some embodiments, the libraries of the present disclosure further comprise meta data associated with the effects of applying each member of the library in host organisms. For example, a library as used herein can include a collection of promoter::gene sequence combinations, together with the resulting effect of those combinations on one or more phenotypes in a particular species, thus improving the future predictive value of using said combination in future promoter swaps.

As used herein, the term “SNP” refers to Small Nuclear Polymorphism(s). In some embodiments, SNPs of the present disclosure should be construed broadly, and include single nucleotide polymorphisms, sequence insertions, deletions, inversions, and other sequence replacements. As used herein, the term “non-synonymous” or non-synonymous SNPs” refers to mutations that lead to coding changes in host cell proteins

A “high-throughput (HTP)” method of genomic engineering may involve the utilization of at least one piece of automated equipment (e.g. a liquid handler or plate handler machine) to carry out at least one step of said method.

Traditional Methods of Strain Improvement

Traditional approaches to strain improvement can be broadly categorized into two types of approaches: directed strain engineering, and random mutagenesis.

Directed engineering methods of strain improvement involve the planned perturbation of a handful of genetic elements of a specific organism. These approaches are typically focused on modulating specific biosynthetic or developmental programs, and rely on prior knowledge of the genetic and metabolic factors affecting said pathways. In its simplest embodiments, directed engineering involves the transfer of a characterized trait (e.g., gene, promoter, or other genetic element capable of producing a measurable phenotype) from one organism to another organism of the same, or different species.

Random approaches to strain engineering involve the random mutagenesis of parent strains, coupled with extensive screening designed to identify performance improvements. Approaches to generating these random mutations include exposure to ultraviolet radiation, or mutagenic chemicals such as Ethyl methanesulfonate. Though random and largely unpredictable, this traditional approach to strain improvement had several advantages compared to more directed genetic manipulations. First, many industrial organisms were (and remain) poorly characterized in terms of their genetic and metabolic repertoires, rendering alternative directed improvement approaches difficult, if not impossible.

Second, even in relatively well characterized systems, genotypic changes that result in industrial performance improvements are difficult to predict, and sometimes only manifest themselves as epistatic phenotypes requiring cumulative mutations in many genes of known and unknown function.

Additionally, for many years, the genetic tools required for making directed genomic mutations in a given industrial organism were unavailable, or very slow and/or difficult to use.

The extended application of the traditional strain improvement programs, however, yield progressively reduced gains in a given strain lineage, and ultimately lead to exhausted possibilities for further strain efficiencies. Beneficial random mutations are relatively rare events, and require large screening pools and high mutation rates. This inevitably results in the inadvertent accumulation of many neutral and/or detrimental (or partly detrimental) mutations in “improved” strains, which ultimately create a drag on future efficiency gains.

Another limitation of traditional cumulative improvement approaches is that little to no information is known about any particular mutation's effect on any strain metric. This fundamentally limits a researcher's ability to combine and consolidate beneficial mutations, or to remove neutral or detrimental mutagenic “baggage.”

Other approaches and technologies exist to randomly recombine mutations between strains within a mutagenic lineage. For example, some formats and examples for iterative sequence recombination, sometimes referred to as DNA shuffling, evolution, or molecular breeding, have been described in U.S. patent application Ser. No. 08/198,431, filed Feb. 17, 1994, Serial No. PCT/US95/02126, filed, Feb. 17, 1995, Ser. No. 08/425,684, filed Apr. 18, 1995, Ser. No. 08/537,874, filed Oct. 30, 1995, Ser. No. 08/564,955, filed Nov. 30, 1995, Ser. No. 08/621,859, filed. Mar. 25, 1996, Ser. No. 08/621,430, filed Mar. 25, 1996, Serial No. PCT/US96/05480, filed Apr. 18, 1996, Ser. No. 08/650,400, filed May 20, 1996, Ser. No. 08/675,502, filed Jul. 3, 1996, Ser. No. 08/721,824, filed Sep. 27, 1996, and Ser. No. 08/722,660 filed Sep. 27, 1996; Stemmer, Science 270:1510 (1995); Stemmer et al., Gene 164:49-53 (1995); Stemmer, Bio/Technology 13:549-553 (1995); Stemmer, Proc. Natl. Acad. Sci. U.S.A. 91:10747-10751 (1994); Stemmer, Nature 370:389-391 (1994); Crameri et al., Nature Medicine 2(1):1-3 (1996); Crameri et al., Nature Biotechnology 14:315-319 (1996), each of which is incorporated herein by reference in its entirety for all purposes.

These include techniques such as protoplast fusion and whole genome shuffling that facilitate genomic recombination across mutated strains. For some industrial microorganisms such as yeast and filamentous fungi, natural mating cycles can also be exploited for pairwise genomic recombination. In this way, detrimental mutations can be removed by ‘back-crossing’ mutants with parental strains and beneficial mutations consolidated. Moreover, beneficial mutations from two different strain lineages can potentially be combined, which creates additional improvement possibilities over what might be available from mutating a single strain lineage on its own. However, these approaches are subject to many limitations that are circumvented using the methods of the present disclosure.

For example, traditional recombinant approaches as described above are slow and rely on a relatively small number of random recombination crossover events to swap mutations, and are therefore limited in the number of combinations that can be attempted in any given cycle, or time period. In addition, although the natural recombination events in the prior art are essentially random, they are also subject to genome positional bias.

Most importantly, the traditional approaches also provide little information about the influence of individual mutations and due to the random distribution of recombined mutations many specific combinations cannot be generated and evaluated.

To overcome many of the aforementioned problems associated with traditional strain improvement programs, the present disclosure sets forth a unique HTP genomic engineering platform that is computationally driven and integrates molecular biology, automation, data analytics, and machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets that are used to construct HTP genetic design libraries. These genetic design libraries will be elaborated upon below.

The taught HTP platform and its unique microbial genetic design libraries fundamentally shift the paradigm of microbial strain development and evolution. For example, traditional mutagenesis-based methods of developing an industrial microbial strain will eventually lead to microbes burdened with a heavy mutagenic load that has been accumulated over years of random mutagenesis.

The ability to solve this issue (i.e. remove the genetic baggage accumulated by these microbes) has eluded microbial researchers for decades. However, utilizing the HTP platform disclosed herein, these industrial strains can be “rehabilitated,” and the genetic mutations that are deleterious can be identified and removed. Congruently, the genetic mutations that are identified as beneficial can be kept, and in some cases improved upon. The resulting microbial strains demonstrate superior phenotypic traits (e.g., improved production of a compound of interest), as compared to their parental strains.

Furthermore, the HTP platform taught herein is able to identify, characterize, and quantify the effect that individual mutations have on microbial strain performance. This information, i.e. what effect does a given genetic change x have on host cell phenotype y (e.g., production of a compound or product of interest), is able to be generated and then stored in the microbial HTP genetic design libraries discussed below. That is, sequence information for each genetic permutation, and its effect on the host cell phenotype are stored in one or more databases, and are available for subsequent analysis (e.g., epistasis mapping, as discussed below). The present disclosure also teaches methods of physically saving/storing valuable genetic permutations in the form of genetic insertion constructs, or in the form of one or more host cell organisms containing said genetic permutation (e.g., see libraries discussed below.)

When one couples these HTP genetic design libraries into an iterative process that is integrated with a sophisticated data analytics and machine learning process a dramatically different methodology for improving host cells emerges. The taught platform is therefore fundamentally different from the previously discussed traditional methods of developing host cell strains. The taught HTP platform does not suffer from many of the drawbacks associated with the previous methods. These and other advantages will become apparent with reference to the HTP molecular tool sets and the derived genetic design libraries discussed below.

Genetic Design & Microbial Engineering: A Systematic Combinatorial Approach to Strain Improvement Utilizing a Suite of HTP Molecular Tools and HTP Genetic Design Libraries

As aforementioned, the present disclosure provides a novel HTP platform and genetic design strategy for engineering microbial organisms through iterative systematic introduction and removal of genetic changes across strains. The platform is supported by a suite of molecular tools, which enable the creation of HTP genetic design libraries and allow for the efficient implementation of genetic alterations into a given host strain.

The HTP genetic design libraries of the disclosure serve as sources of possible genetic alterations that may be introduced into a particular microbial strain background. In this way, the HTP genetic design libraries are repositories of genetic diversity, or collections of genetic perturbations, which can be applied to the initial or further engineering of a given microbial strain. Techniques for programming genetic designs for implementation to host strains are described in pending U.S. patent application Ser. No. 15/140,296, entitled “Microbial Strain Design System and Methods for Improved Large Scale Production of Engineered Nucleotide Sequences,” incorporated by reference in its entirety herein.

The HTP molecular tool sets utilized in this platform may include, inter alia: (1) Promoter swaps (PRO Swap), (2) SNP swaps, (3) Start/Stop codon exchanges, (4) STOP swaps, and (5) Sequence optimization. The HTP methods of the present disclosure also teach methods for directing the consolidation/combinatorial use of HTP tool sets, including (6) Epistasis mapping protocols. As aforementioned, this suite of molecular tools, either in isolation or combination, enables the creation of HTP genetic design host cell libraries.

As will be demonstrated, utilization of the aforementioned HTP genetic design libraries in the context of the taught HTP microbial engineering platform enables the identification and consolidation of beneficial “causative” mutations or gene sections and also the identification and removal of passive or detrimental mutations or gene sections. This new approach allows rapid improvements in strain performance that could not be achieved by traditional random mutagenesis or directed genetic engineering. The removal of genetic burden or consolidation of beneficial changes into a strain with no genetic burden also provides a new, robust starting point for additional random mutagenesis that may enable further improvements.

In some embodiments, the present disclosure teaches that as orthogonal beneficial changes are identified across various, discrete branches of a mutagenic strain lineage, they can also be rapidly consolidated into better performing strains. These mutations can also be consolidated into strains that are not part of mutagenic lineages, such as strains with improvements gained by directed genetic engineering.

In some embodiments, the present disclosure differs from known strain improvement approaches in that it analyzes the genome-wide combinatorial effect of mutations across multiple disparate genomic regions, including expressed and non-expressed genetic elements, and uses gathered information (e.g., experimental results) to predict mutation combinations expected to produce strain enhancements.

In some embodiments, the present disclosure teaches: i) industrial microorganisms, and other host cells amenable to improvement via the disclosed inventions, ii) generating diversity pools for downstream analysis, iii) methods and hardware for high-throughput screening and sequencing of large variant pools, iv) methods and hardware for machine learning computational analysis and prediction of synergistic effects of genome-wide mutations, and v) methods for high-throughput strain engineering.

The following molecular tools and libraries are discussed in terms of illustrative microbial examples. Persons having skill in the art will recognize that the HTP molecular tools of the present disclosure are compatible with any host cell, including eukaryotic cellular, and higher life forms.

Each of the identified HTP molecular tool sets—which enable the creation of the various HTP genetic design libraries utilized in the microbial engineering platform—will now be discussed.

1. Promoter Swaps: A Molecular Tool for the Derivation of Promoter Swap Microbial Strain Libraries

In some embodiments, the present disclosure teaches methods of selecting promoters with optimal expression properties to produce beneficial effects on overall-host strain phenotype (e.g., yield or productivity).

For example, in some embodiments, the present disclosure teaches methods of identifying one or more promoters and/or generating variants of one or more promoters within a host cell, which exhibit a range of expression strengths (e.g. promoter ladders discussed infra), or superior regulatory properties (e.g., tighter regulatory control for selected genes). A particular combination of these identified and/or generated promoters can be grouped together as a promoter ladder, which is explained in more detail below.

The promoter ladder in question is then associated with a given gene of interest. Thus, if one has promoters P₁-P₈ (representing eight promoters that have been identified and/or generated to exhibit a range of expression strengths) and associates the promoter ladder with a single gene of interest in a microbe (i.e. genetically engineer a microbe with a given promoter operably linked to a given target gene), then the effect of each combination of the eight promoters can be ascertained by characterizing each of the engineered strains resulting from each combinatorial effort, given that the engineered microbes have an otherwise identical genetic background except the particular promoter(s) associated with the target gene.

The resultant microbes that are engineered via this process form HTP genetic design libraries.

The HTP genetic design library can refer to the actual physical microbial strain collection that is formed via this process, with each member strain being representative of a given promoter operably linked to a particular target gene, in an otherwise identical genetic background, said library being termed a “promoter swap microbial strain library.”

Furthermore, the HTP genetic design library can refer to the collection of genetic perturbations—in this case a given promoter x operably linked to a given gene y—said collection being termed a “promoter swap library.”

Further, one can utilize the same promoter ladder comprising promoters P₁-P₈ to engineer microbes, wherein each of the 8 promoters is operably linked to 10 different gene targets. The result of this procedure would be 80 microbes that are otherwise assumed genetically identical, except for the particular promoters operably linked to a target gene of interest. These 80 microbes could be appropriately screened and characterized and give rise to another HTP genetic design library. The characterization of the microbial strains in the HTP genetic design library produces information and data that can be stored in any data storage construct, including a relational database, an object-oriented database or a highly distributed NoSQL database. This data/information could be, for example, a given promoter's (e.g. P₁-P₈) effect when operably linked to a given gene target. This data/information can also be the broader set of combinatorial effects that result from operably linking two or more of promoters P₁-P₈ to a given gene target.

The aforementioned examples of eight promoters and 10 target genes is merely illustrative, as the concept can be applied with any given number of promoters that have been grouped together based upon exhibition of a range of expression strengths and any given number of target genes. Persons having skill in the art will also recognize the ability to operably link two or more promoters in front of any gene target. Thus, in some embodiments, the present disclosure teaches promoter swap libraries in which 1, 2, 3 or more promoters from a promoter ladder are operably linked to one or more genes.

In summary, utilizing various promoters to drive expression of various genes in an organism is a powerful tool to optimize a trait of interest. The molecular tool of promoter swapping, developed by the inventors, uses a ladder of promoter sequences that have been demonstrated to vary expression of at least one locus under at least one condition. This ladder is then systematically applied to a group of genes in the organism using high-throughput genome engineering. This group of genes is determined to have a high likelihood of impacting the trait of interest based on any one of a number of methods. These could include selection based on known function, or impact on the trait of interest, or algorithmic selection based on previously determined beneficial genetic diversity. In some embodiments, the selection of genes can include all the genes in a given host. In other embodiments, the selection of genes can be a subset of all genes in a given host, chosen randomly.

The resultant HTP genetic design microbial strain library of organisms containing a promoter sequence linked to a gene is then assessed for performance in a high-throughput screening model, and promoter-gene linkages which lead to increased performance are determined and the information stored in a database. The collection of genetic perturbations (i.e. given promoter x operably linked to a given gene y) form a “promoter swap library,” which can be utilized as a source of potential genetic alterations to be utilized in microbial engineering processing. Over time, as a greater set of genetic perturbations is implemented against a greater diversity of host cell backgrounds, each library becomes more powerful as a corpus of experimentally confirmed data that can be used to more precisely and predictably design targeted changes against any background of interest.

Transcription levels of genes in an organism are a key point of control for affecting organism behavior. Transcription is tightly coupled to translation (protein expression), and which proteins are expressed in what quantities determines organism behavior. Cells express thousands of different types of proteins, and these proteins interact in numerous complex ways to create function. By varying the expression levels of a set of proteins systematically, function can be altered in ways that, because of complexity, are difficult to predict. Some alterations may increase performance, and so, coupled to a mechanism for assessing performance, this technique allows for the generation of organisms with improved function.

In the context of a small molecule synthesis pathway, enzymes interact through their small molecule substrates and products in a linear or branched chain, starting with a substrate and ending with a small molecule of interest. Because these interactions are sequentially linked, this system exhibits distributed control, and increasing the expression of one enzyme can only increase pathway flux until another enzyme becomes rate limiting.

Metabolic Control Analysis (MCA) is a method for determining, from experimental data and first principles, which enzyme or enzymes are rate limiting. MCA is limited however, because it requires extensive experimentation after each expression level change to determine the new rate limiting enzyme. Promoter swapping is advantageous in this context, because through the application of a promoter ladder to each enzyme in a pathway, the limiting enzyme is found, and the same thing can be done in subsequent rounds to find new enzymes that become rate limiting. Further, because the read-out on function is better production of the small molecule of interest, the experiment to determine which enzyme is limiting is the same as the engineering to increase production, thus shortening development time. In some embodiments the present disclosure teaches the application of PRO swap to genes encoding individual subunits of multi-unit enzymes. In yet other embodiments, the present disclosure teaches methods of applying PRO swap techniques to genes responsible for regulating individual enzymes, or whole biosynthetic pathways.

In some embodiments, the promoter swap tool of the present disclosure can is used to identify optimum expression of a selected gene target. In some embodiments, the goal of the promoter swap may be to increase expression of a target gene to reduce bottlenecks in a metabolic or genetic pathway. In other embodiments, the goal to the promoter swap may be to reduce the expression of the target gene to avoid unnecessary energy expenditures in the host cell, when expression of said target gene is not required.

In the context of other cellular systems like transcription, transport, or signaling, various rational methods can be used to try and find out, a priori, which proteins are targets for expression change and what that change should be. These rational methods reduce the number of perturbations that must be tested to find one that improves performance, but they do so at significant cost. Gene deletion studies identify proteins whose presence is critical for a particular function, and important genes can then be over-expressed. Due to the complexity of protein interactions, this is often ineffective at increasing performance. Different types of models have been developed that attempt to describe, from first principles, transcription or signaling behavior as a function of protein levels in the cell. These models often suggest targets where expression changes might lead to different or improved function. The assumptions that underlie these models are simplistic and the parameters difficult to measure, so the predictions they make are often incorrect, especially for non-model organisms. With both gene deletion and modeling, the experiments required to determine how to affect a certain gene are different than the subsequent work to make the change that improves performance. Promoter swapping sidesteps these challenges, because the constructed strain that highlights the importance of a particular perturbation is also, already, the improved strain.

Thus, in particular embodiments, promoter swapping is a multi-step process comprising:

1. Selecting a set of “x” promoters to act as a “ladder.” Ideally these promoters have been shown to lead to highly variable expression across multiple genomic loci, but the only requirement is that they perturb gene expression in some way.

2. Selecting a set of “n” genes to target. This set can be every open reading frame (ORF) in a genome, or a subset of ORFs. The subset can be chosen using annotations on ORFs related to function, by relation to previously demonstrated beneficial perturbations (previous promoter swaps or previous SNP swaps), by algorithmic selection based on epistatic interactions between previously generated perturbations, other selection criteria based on hypotheses regarding beneficial ORF to target, or through random selection. In other embodiments, the “n” targeted genes can comprise non-protein coding genes, including non-coding RNAs.

3. High-throughput strain engineering to rapidly- and in some embodiments, in parallel-carry out the following genetic modifications: When a native promoter exists in front of target gene n and its sequence is known, replace the native promoter with each of the x promoters in the ladder. When the native promoter does not exist, or its sequence is unknown, insert each of the x promoters in the ladder in front of gene n (see e.g., FIG. 21). In this way a “library” (also referred to as a HTP genetic design library) of strains is constructed, wherein each member of the library is an instance of x promoter operably linked to n target, in an otherwise identical genetic context. As previously described combinations of promoters can be inserted, extending the range of combinatorial possibilities upon which the library is constructed.

4. High-throughput screening of the library of strains in a context where their performance against one or more metrics is indicative of the performance that is being optimized.

This foundational process can be extended to provide further improvements in strain performance by, inter alia: (1) Consolidating multiple beneficial perturbations into a single strain background, either one at a time in an interactive process, or as multiple changes in a single step. Multiple perturbations can be either a specific set of defined changes or a partly randomized, combinatorial library of changes. For example, if the set of targets is every gene in a pathway, then sequential regeneration of the library of perturbations into an improved member or members of the previous library of strains can optimize the expression level of each gene in a pathway regardless of which genes are rate limiting at any given iteration; (2) Feeding the performance data resulting from the individual and combinatorial generation of the library into an algorithm that uses that data to predict an optimum set of perturbations based on the interaction of each perturbation; and (3) Implementing a combination of the above two approaches (see FIG. 20).

The molecular tool, or technique, discussed above is characterized as promoter swapping, but is not limited to promoters and can include other sequence changes that systematically vary the expression level of a set of targets. Other methods for varying the expression level of a set of genes could include: a) a ladder of ribosome binding sites (or Kozak sequences in eukaryotes); b) replacing the start codon of each target with each of the other start codons (i.e start/stop codon exchanges discussed infra); c) attachment of various mRNA stabilizing or destabilizing sequences to the 5′ or 3′ end, or at any other location, of a transcript, d) attachment of various protein stabilizing or destabilizing sequences at any location in the protein.

The approach is exemplified in the present disclosure with industrial microorganisms, but is applicable to any organism where desired traits can be identified in a population of genetic mutants. For example, this could be used for improving the performance of CHO cells, yeast, insect cells, algae, as well as multi-cellular organisms, such as plants.

2. SNP Swaps: A Molecular Tool for the Derivation of SNP Swap Microbial Strain Libraries

In certain embodiments, SNP swapping is not a random mutagenic approach to improving a microbial strain, but rather involves the systematic introduction or removal of individual Small Nuclear Polymorphism nucleotide mutations (i.e. SNPs) (hence the name “SNP swapping”) across strains.

The resultant microbes that are engineered via this process form HTP genetic design libraries.

The HTP genetic design library can refer to the actual physical microbial strain collection that is formed via this process, with each member strain being representative of the presence or absence of a given SNP, in an otherwise identical genetic background, said library being termed a “SNP swap microbial strain library.”

Furthermore, the HTP genetic design library can refer to the collection of genetic perturbations—in this case a given SNP being present or a given SNP being absent—said collection being termed a “SNP swap library.”

In some embodiments, SNP swapping involves the reconstruction of host organisms with optimal combinations of target SNP “building blocks” with identified beneficial performance effects. Thus, in some embodiments, SNP swapping involves consolidating multiple beneficial mutations into a single strain background, either one at a time in an iterative process, or as multiple changes in a single step. Multiple changes can be either a specific set of defined changes or a partly randomized, combinatorial library of mutations.

In other embodiments, SNP swapping also involves removing multiple mutations identified as detrimental from a strain, either one at a time in an iterative process, or as multiple changes in a single step. Multiple changes can be either a specific set of defined changes or a partly randomized, combinatorial library of mutations. In some embodiments, the SNP swapping methods of the present disclosure include both the addition of beneficial SNPs, and removing detrimental and/or neutral mutations.

SNP swapping is a powerful tool to identify and exploit both beneficial and detrimental mutations in a lineage of strains subjected to mutagenesis and selection for an improved trait of interest. SNP swapping utilizes high-throughput genome engineering techniques to systematically determine the influence of individual mutations in a mutagenic lineage. Genome sequences are determined for strains across one or more generations of a mutagenic lineage with known performance improvements. High-throughput genome engineering is then used systematically to recapitulate mutations from improved strains in earlier lineage strains, and/or revert mutations in later strains to earlier strain sequences. The performance of these strains is then evaluated and the contribution of each individual mutation on the improved phenotype of interest can be determined. As aforementioned, the microbial strains that result from this process are analyzed/characterized and form the basis for the SNP swap genetic design libraries that can inform microbial strain improvement across host strains.

Removal of detrimental mutations can provide immediate performance improvements, and consolidation of beneficial mutations in a strain background not subject to mutagenic burden can rapidly and greatly improve strain performance. The various microbial strains produced via the SNP swapping process form the HTP genetic design SNP swapping libraries, which are microbial strains comprising the various added/deleted/or consolidated SNPs, but with otherwise identical genetic backgrounds.

As discussed previously, random mutagenesis and subsequent screening for performance improvements is a commonly used technique for industrial strain improvement, and many strains currently used for large scale manufacturing have been developed using this process iteratively over a period of many years, sometimes decades. Random approaches to generating genomic mutations such as exposure to UV radiation or chemical mutagens such as ethyl methanesulfonate were a preferred method for industrial strain improvements because: 1) industrial organisms may be poorly characterized genetically or metabolically, rendering target selection for directed improvement approaches difficult or impossible; 2) even in relatively well characterized systems, changes that result in industrial performance improvements are difficult to predict and may require perturbation of genes that have no known function, and 3) genetic tools for making directed genomic mutations in a given industrial organism may not be available or very slow and/or difficult to use.

However, despite the aforementioned benefits of this process, there are also a number of known disadvantages. Beneficial mutations are relatively rare events, and in order to find these mutations with a fixed screening capacity, mutations rates must be sufficiently high. This often results in unwanted neutral and partly detrimental mutations being incorporated into strains along with beneficial changes. Over time this ‘mutagenic burden’ builds up, resulting in strains with deficiencies in overall robustness and key traits such as growth rates. Eventually ‘mutagenic burden’ renders further improvements in performance through random mutagenesis increasingly difficult or impossible to obtain. Without suitable tools, it is impossible to consolidate beneficial mutations found in discrete and parallel branches of strain lineages.

SNP swapping is an approach to overcome these limitations by systematically recapitulating or reverting some or all mutations observed when comparing strains within a mutagenic lineage. In this way, both beneficial (‘causative’) mutations can be identified and consolidated, and/or detrimental mutations can be identified and removed. This allows rapid improvements in strain performance that could not be achieved by further random mutagenesis or targeted genetic engineering.

Removal of genetic burden or consolidation of beneficial changes into a strain with no genetic burden also provides a new, robust starting point for additional random mutagenesis that may enable further improvements.

In addition, as orthogonal beneficial changes are identified across various, discrete branches of a mutagenic strain lineage, they can be rapidly consolidated into better performing strains. These mutations can also be consolidated into strains that are not part of mutagenic lineages, such as strains with improvements gained by directed genetic engineering.

Other approaches and technologies exist to randomly recombine mutations between strains within a mutagenic lineage. These include techniques such as protoplast fusion and whole genome shuffling that facilitate genomic recombination across mutated strains. For some industrial microorganisms such as yeast and filamentous fungi, natural mating cycles can also be exploited for pairwise genomic recombination. In this way, detrimental mutations can be removed by ‘back-crossing’ mutants with parental strains and beneficial mutations consolidated. However, these approaches are subject to many limitations that are circumvented using the SNP swapping methods of the present disclosure.

For example, as these approaches rely on a relatively small number of random recombination crossover events to swap mutations, it may take many cycles of recombination and screening to optimize strain performance. In addition, although natural recombination events are essentially random, they are also subject to genome positional bias and some mutations may be difficult to address. These approaches also provide little information about the influence of individual mutations without additional genome sequencing and analysis. SNP swapping overcomes these fundamental limitations as it is not a random approach, but rather the systematic introduction or removal of individual mutations across strains.

In some embodiments, the present disclosure teaches methods for identifying the SNP sequence diversity present among the organisms of a diversity pool. A diversity pool can be a given number n of microbes utilized for analysis, with said microbes' genomes representing the “diversity pool.”

In particular aspects, a diversity pool may be an original parent strain (S₁) with a “baseline” or “reference” genetic sequence at a particular time point (S₁Gen₁) and then any number of subsequent offspring strains (S_(2-n)) that were derived/developed from said S₁ strain and that have a different genome (S_(2-n)Gen_(2-n)), in relation to the baseline genome of S₁.

For example, in some embodiments, the present disclosure teaches sequencing the microbial genomes in a diversity pool to identify the SNPs present in each strain. In one embodiment, the strains of the diversity pool are historical microbial production strains. Thus, a diversity pool of the present disclosure can include for example, an industrial reference strain, and one or more mutated industrial strains produced via traditional strain improvement programs.

In some embodiments, the SNPs within a diversity pool are determined with reference to a “reference strain.” In some embodiments, the reference strain is a wild-type strain. In other embodiments, the reference strain is an original industrial strain prior to being subjected to any mutagenesis. The reference strain can be defined by the practitioner and does not have to be an original wild-type strain or original industrial strain. The base strain is merely representative of what will be considered the “base,” “reference” or original genetic background, by which subsequent strains that were derived, or were developed from said reference strain, are to be compared.

Once all SNPS in the diversity pool are identified, the present disclosure teaches methods of SNP swapping and screening methods to delineate (i.e. quantify and characterize) the effects (e.g. creation of a phenotype of interest) of SNPs individually and/or in groups.

In some embodiments, the SNP swapping methods of the present disclosure comprise the step of introducing one or more SNPs identified in a mutated strain (e.g., a strain from amongst S_(2-n)Gen_(2-n)) to a reference strain (S₁Gen₁) or wild-type strain (“wave up”).

In other embodiments, the SNP swapping methods of the present disclosure comprise the step of removing one or more SNPs identified in a mutated strain (e.g., a strain from amongst S_(2-n)Gen_(2-n)) (“wave down”).

In some embodiments, each generated strain comprising one or more SNP changes (either introducing or removing) is cultured and analyzed under one or more criteria of the present disclosure (e.g., production of a chemical or product of interest). Data from each of the analyzed host strains is associated, or correlated, with the particular SNP, or group of SNPs present in the host strain, and is recorded for future use. Thus, the present disclosure enables the creation of large and highly annotated HTP genetic design microbial strain libraries that are able to identify the effect of a given SNP on any number of microbial genetic or phenotypic traits of interest. The information stored in these HTP genetic design libraries informs the machine learning algorithms of the HTP genomic engineering platform and directs future iterations of the process, which ultimately leads to evolved microbial organisms that possess highly desirable properties/traits.

3. Start/Stop Codon Exchanges: A Molecular Tool for the Derivation of Start/Stop Codon Microbial Strain Libraries

In some embodiments, the present disclosure teaches methods of swapping start and stop codon variants. For example, typical stop codons for S. cerevisiae and mammals are TAA (UAA) and TGA (UGA), respectively. The typical stop codon for monocotyledonous plants is TGA (UGA), whereas insects and E. coli commonly use TAA (UAA) as the stop codon (Dalphin et al. (1996) Nucl. Acids Res. 24: 216-218). In other embodiments, the present disclosure teaches use of the TAG (UAG) stop codons.

The present disclosure similarly teaches swapping start codons. In some embodiments, the present disclosure teaches use of the ATG (AUG) start codon utilized by most organisms (especially eukaryotes). In some embodiments, the present disclosure teaches that prokaryotes use ATG (AUG) the most, followed by GTG (GUG) and TTG (UUG).

In other embodiments, the present invention teaches replacing ATG start codons with TTG. In some embodiments, the present invention teaches replacing ATG start codons with GTG. In some embodiments, the present invention teaches replacing GTG start codons with ATG. In some embodiments, the present invention teaches replacing GTG start codons with TTG. In some embodiments, the present invention teaches replacing TTG start codons with ATG. In some embodiments, the present invention teaches replacing TTG start codons with GTG.

In other embodiments, the present invention teaches replacing TAA stop codons with TAG. In some embodiments, the present invention teaches replacing TAA stop codons with TGA. In some embodiments, the present invention teaches replacing TGA stop codons with TAA. In some embodiments, the present invention teaches replacing TGA stop codons with TAG. In some embodiments, the present invention teaches replacing TAG stop codons with TAA. In some embodiments, the present invention teaches replacing TAG stop codons with TGA.

4. Stop swap: A Molecular Tool for the Derivation of Optimized Sequence Microbial Strain Libraries

In some embodiments, the present disclosure teaches methods of improving host cell productivity through the optimization of cellular gene transcription. Gene transcription is the result of several distinct biological phenomena, including transcriptional initiation (RNAp recruitment and transcriptional complex formation), elongation (strand synthesis/extension), and transcriptional termination (RNAp detachment and termination). Although much attention has been devoted to the control of gene expression through the transcriptional modulation of genes (e.g., by changing promoters, or inducing regulatory transcription factors), comparatively few efforts have been made towards the modulation of transcription via the modulation of gene terminator sequences.

The most obvious way that transcription impacts on gene expression levels is through the rate of Pol II initiation, which can be modulated by combinations of promoter or enhancer strength and trans-activating factors (Kadonaga, J T. 2004 “Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors” Cell. 2004 Jan. 23; 116(2):247-57). In eukaryotes, elongation rate may also determine gene expression patterns by influencing alternative splicing (Cramer P. et al., 1997 “Functional association between promoter structure and transcript alternative splicing.” Proc Natl Acad Sci USA. 1997 Oct. 14; 94(21):11456-60). Failed termination on a gene can impair the expression of downstream genes by reducing the accessibility of the promoter to Pol II (Greger I H. et al., 2000 “Balancing transcriptional interference and initiation on the GAL7 promoter of Saccharomyces cerevisiae.” Proc Natl Acad Sci USA. 2000 Jul. 18; 97(15):8415-20). This process, known as transcriptional interference, is particularly relevant in lower eukaryotes, as they often have closely spaced genes.

Termination sequences can also affect the expression of the genes to which the sequences belong. For example, studies show that inefficient transcriptional termination in eukaryotes results in an accumulation of unspliced pre-mRNA (see West, S., and Proudfoot, N.J., 2009 “Transcriptional Termination Enhances Protein Expression in Human Cells” Mol Cell. 2009 Feb. 13; 33(3-9); 354-364). Other studies have also shown that 3′ end processing, can be delayed by inefficient termination (West, S et al., 2008 “Molecular dissection of mammalian RNA polymerase II transcriptional termination.” Mol Cell. 2008 Mar. 14; 29(5):600-10.). Transcriptional termination can also affect mRNA stability by releasing transcripts from sites of synthesis.

Termination of Transcription Mechanism in Eukaryotes

Transcriptional termination in eukaryotes operates through terminator signals that are recognized by protein factors associated with the RNA polymerase II. In some embodiments, the cleavage and polyadenylation specificity factor (CPSF) and cleavage stimulation factor (CstF) transfer from the carboxyl terminal domain of RNA polymerase II to the poly-A signal. In some embodiments, the CPSF and CstF factors also recruit other proteins to the termination site, which then cleave the transcript and free the mRNA from the transcription complex. Termination also triggers polyadenylation of mRNA transcripts. Illustrative examples of validated eukaryotic termination factors, and their conserved structures are discussed in later portions of this document.

Termination of Transcription in Prokaryotes

In prokaryotes, two principal mechanisms, termed Rho-independent and Rho-dependent termination, mediate transcriptional termination. Rho-independent termination signals do not require an extrinsic transcription-termination factor, as formation of a stem-loop structure in the RNA transcribed from these sequences along with a series of Uridine (U) residues promotes release of the RNA chain from the transcription complex. Rho-dependent termination, on the other hand, requires a transcription-termination factor called Rho and cis-acting elements on the mRNA. The initial binding site for Rho, the Rho utilization (rut) site, is an extended C70 nucleotides, sometimes 80-100 nucleotides) single-stranded region characterized by a high cytidine/low guanosine content and relatively little secondary structure in the RNA being synthesized, upstream of the actual terminator sequence. When a polymerase pause site is encountered, termination occurs, and the transcript is released by Rho's helicase activity.

Terminator Swapping (STOP Swap)

In some embodiments, the present disclosure teaches methods of selecting termination sequences (“terminators”) with optimal expression properties to produce beneficial effects on overall-host strain productivity.

For example, in some embodiments, the present disclosure teaches methods of identifying one or more terminators and/or generating variants of one or more terminators within a host cell, which exhibit a range of expression strengths (e.g. terminator ladders discussed infra). A particular combination of these identified and/or generated terminators can be grouped together as a terminator ladder, which is explained in more detail below.

The terminator ladder in question is then associated with a given gene of interest. Thus, if one has terminators T₁-T₈ (representing eight terminators that have been identified and/or generated to exhibit a range of expression strengths when combined with one or more promoters) and associates the terminator ladder with a single gene of interest in a host cell (i.e. genetically engineer a host cell with a given terminator operably linked to the 3′ end of to a given target gene), then the effect of each combination of the terminators can be ascertained by characterizing each of the engineered strains resulting from each combinatorial effort, given that the engineered host cells have an otherwise identical genetic background except the particular promoter(s) associated with the target gene. The resultant host cells that are engineered via this process form HTP genetic design libraries.

The HTP genetic design library can refer to the actual physical microbial strain collection that is formed via this process, with each member strain being representative of a given terminator operably linked to a particular target gene, in an otherwise identical genetic background, said library being termed a “terminator swap microbial strain library” or “STOP swap microbial strain library.”

Furthermore, the HTP genetic design library can refer to the collection of genetic perturbations—in this case a given terminator x operably linked to a given gene y—said collection being termed a “terminator swap library” or “STOP swap library.”

Further, one can utilize the same terminator ladder comprising promoters T₁-T₈ to engineer microbes, wherein each of the eight terminators is operably linked to 10 different gene targets. The result of this procedure would be 80 host cell strains that are otherwise assumed genetically identical, except for the particular terminators operably linked to a target gene of interest. These 80 host cell strains could be appropriately screened and characterized and give rise to another HTP genetic design library. The characterization of the microbial strains in the HTP genetic design library produces information and data that can be stored in any database, including without limitation, a relational database, an object-oriented database or a highly distributed NoSQL database. This data/information could include, for example, a given terminators' (e.g., T₁-T₈) effect when operably linked to a given gene target. This data/information can also be the broader set of combinatorial effects that result from operably linking two or more of promoters T₁-T₈ to a given gene target.

The aforementioned examples of eight terminators and 10 target genes is merely illustrative, as the concept can be applied with any given number of promoters that have been grouped together based upon exhibition of a range of expression strengths and any given number of target genes.

In summary, utilizing various terminators to modulate expression of various genes in an organism is a powerful tool to optimize a trait of interest. The molecular tool of terminator swapping, developed by the inventors, uses a ladder of terminator sequences that have been demonstrated to vary expression of at least one locus under at least one condition. This ladder is then systematically applied to a group of genes in the organism using high-throughput genome engineering. This group of genes is determined to have a high likelihood of impacting the trait of interest based on any one of a number of methods. These could include selection based on known function, or impact on the trait of interest, or algorithmic selection based on previously determined beneficial genetic diversity.

The resultant HTP genetic design microbial library of organisms containing a terminator sequence linked to a gene is then assessed for performance in a high-throughput screening model, and promoter-gene linkages which lead to increased performance are determined and the information stored in a database. The collection of genetic perturbations (i.e. given terminator x linked to a given gene y) form a “terminator swap library,” which can be utilized as a source of potential genetic alterations to be utilized in microbial engineering processing. Over time, as a greater set of genetic perturbations is implemented against a greater diversity of microbial backgrounds, each library becomes more powerful as a corpus of experimentally confirmed data that can be used to more precisely and predictably design targeted changes against any background of interest. That is in some embodiments, the present disclosures teaches introduction of one or more genetic changes into a host cell based on previous experimental results embedded within the meta data associated with any of the genetic design libraries of the invention.

Thus, in particular embodiments, terminator swapping is a multi-step process comprising:

1. Selecting a set of “x” terminators to act as a “ladder.” Ideally these terminators have been shown to lead to highly variable expression across multiple genomic loci, but the only requirement is that they perturb gene expression in some way.

2. Selecting a set of “n” genes to target. This set can be every ORF in a genome, or a subset of ORFs. The subset can be chosen using annotations on ORFs related to function, by relation to previously demonstrated beneficial perturbations (previous promoter swaps, STOP swaps, or SNP swaps), by algorithmic selection based on epistatic interactions between previously generated perturbations, other selection criteria based on hypotheses regarding beneficial ORF to target, or through random selection. In other embodiments, the “n” targeted genes can comprise non-protein coding genes, including non-coding RNAs.

3. High-throughput strain engineering to rapidly and in parallel carry out the following genetic modifications: When a native terminator exists at the 3′ end of target gene n and its sequence is known, replace the native terminator with each of the x terminators in the ladder. When the native terminator does not exist, or its sequence is unknown, insert each of the x terminators in the ladder after the gene stop codon.

In this way a “library” (also referred to as a HTP genetic design library) of strains is constructed, wherein each member of the library is an instance of x terminator linked to n target, in an otherwise identical genetic context. As previously described, combinations of terminators can be inserted, extending the range of combinatorial possibilities upon which the library is constructed.

4. High-throughput screening of the library of strains in a context where their performance against one or more metrics is indicative of the performance that is being optimized.

This foundational process can be extended to provide further improvements in strain performance by, inter alia: (1) Consolidating multiple beneficial perturbations into a single strain background, either one at a time in an interactive process, or as multiple changes in a single step. Multiple perturbations can be either a specific set of defined changes or a partly randomized, combinatorial library of changes. For example, if the set of targets is every gene in a pathway, then sequential regeneration of the library of perturbations into an improved member or members of the previous library of strains can optimize the expression level of each gene in a pathway regardless of which genes are rate limiting at any given iteration; (2) Feeding the performance data resulting from the individual and combinatorial generation of the library into an algorithm that uses that data to predict an optimum set of perturbations based on the interaction of each perturbation; and (3) Implementing a combination of the above two approaches.

The approach is exemplified in the present disclosure with industrial microorganisms, but is applicable to any organism where desired traits can be identified in a population of genetic mutants. For example, this could be used for improving the performance of CHO cells, yeast, insect cells, algae, as well as multi-cellular organisms, such as plants.

5. Sequence Optimization: A Molecular Tool for the Derivation of Optimized Sequence Microbial Strain Libraries

In one embodiment, the methods of the provided disclosure comprise codon optimizing one or more genes expressed by the host organism. Methods for optimizing codons to improve expression in various hosts are known in the art and are described in the literature (see U.S. Pat. App. Pub. No. 2007/0292918, incorporated herein by reference in its entirety). Optimized coding sequences containing codons preferred by a particular prokaryotic or eukaryotic host (see also, Murray et al. (1989) Nucl. Acids Res. 17:477-508) can be prepared, for example, to increase the rate of translation or to produce recombinant RNA transcripts having desirable properties, such as a longer half-life, as compared with transcripts produced from a non-optimized sequence.

Protein expression is governed by a host of factors including those that affect transcription, mRNA processing, and stability and initiation of translation. Optimization can thus address any of a number of sequence features of any particular gene. As a specific example, a rare codon induced translational pause can result in reduced protein expression. A rare codon induced translational pause includes the presence of codons in the polynucleotide of interest that are rarely used in the host organism may have a negative effect on protein translation due to their scarcity in the available tRNA pool.

Alternate translational initiation also can result in reduced heterologous protein expression. Alternate translational initiation can include a synthetic polynucleotide sequence inadvertently containing motifs capable of functioning as a ribosome binding site (RBS). These sites can result in initiating translation of a truncated protein from a gene-internal site. One method of reducing the possibility of producing a truncated protein, which can be difficult to remove during purification, includes eliminating putative internal RBS sequences from an optimized polynucleotide sequence.

Repeat-induced polymerase slippage can result in reduced heterologous protein expression. Repeat-induced polymerase slippage involves nucleotide sequence repeats that have been shown to cause slippage or stuttering of DNA polymerase which can result in frameshift mutations. Such repeats can also cause slippage of RNA polymerase. In an organism with a high G+C content bias, there can be a higher degree of repeats composed of G or C nucleotide repeats. Therefore, one method of reducing the possibility of inducing RNA polymerase slippage, includes altering extended repeats of G or C nucleotides.

Interfering secondary structures also can result in reduced heterologous protein expression. Secondary structures can sequester the RBS sequence or initiation codon and have been correlated to a reduction in protein expression. Stemloop structures can also be involved in transcriptional pausing and attenuation. An optimized polynucleotide sequence can contain minimal secondary structures in the RBS and gene coding regions of the nucleotide sequence to allow for improved transcription and translation.

For example, the optimization process can begin by identifying the desired amino acid sequence to be expressed by the host. From the amino acid sequence a candidate polynucleotide or DNA sequence can be designed. During the design of the synthetic DNA sequence, the frequency of codon usage can be compared to the codon usage of the host expression organism and rare host codons can be removed from the synthetic sequence. Additionally, the synthetic candidate DNA sequence can be modified in order to remove undesirable enzyme restriction sites and add or remove any desired signal sequences, linkers or untranslated regions. The synthetic DNA sequence can be analyzed for the presence of secondary structure that may interfere with the translation process, such as G/C repeats and stem-loop structures.

6. Epistasis Mapping—A Predictive Analytical Tool Enabling Beneficial Genetic Consolidations

In some embodiments, the present disclosure teaches epistasis mapping methods for predicting and combining beneficial genetic alterations into a host cell. The genetic alterations may be created by any of the aforementioned HTP molecular tool sets (e.g., promoter swaps, SNP swaps, start/stop codon exchanges, sequence optimization) and the effect of those genetic alterations would be known from the characterization of the derived HTP genetic design microbial strain libraries. Thus, as used herein, the term epistasis mapping includes methods of identifying combinations of genetic alterations (e.g., beneficial SNPs or beneficial promoter/target gene associations) that are likely to yield increases in host performance.

In embodiments, the epistasis mapping methods of the present disclosure are based on the idea that the combination of beneficial mutations from two different functional groups is more likely to improve host performance, as compared to a combination of mutations from the same functional group. See, e.g., Costanzo, The Genetic Landscape of a Cell, Science, Vol. 327, Issue 5964, Jan. 22, 2010, pp. 425-431 (incorporated by reference herein in its entirety).

Mutations from the same functional group are more likely to operate by the same mechanism, and are thus more likely to exhibit negative or neutral epistasis on overall host performance. In contrast, mutations from different functional groups are more likely to operate by independent mechanisms, which can lead to improved host performance and in some instances synergistic effects. For example, referring to FIG. 19, lysA and zwf are genes that operate in different pathways to achieve the production of lysine. Based upon the dissimilarity in the individual performance of those genes, genetic changes using those genes should result in additive consolidation effects. This was borne out in the actual measurement of the consolidated effects of the combination of lysA and zwf, as shown in FIG. 16B and Examples 6.

Thus, in some embodiments, the present disclosure teaches methods of analyzing SNP mutations to identify SNPs predicted to belong to different functional groups. In some embodiments, SNP functional group similarity is determined by computing the cosine similarity of mutation interaction profiles (similar to a correlation coefficient, see FIG. 16A). The present disclosure also illustrates comparing SNPs via a mutation similarity matrix (see FIG. 15) or dendrogram (see FIG. 16A).

Thus, the epistasis mapping procedure provides a method for grouping and/or ranking a diversity of genetic mutations applied in one or more genetic backgrounds for the purposes of efficient and effective consolidations of said mutations into one or more genetic backgrounds.

In aspects, consolidation is performed with the objective of creating novel strains which are optimized for the production of target biomolecules. Through the taught epistasis mapping procedure, it is possible to identify functional groupings of mutations, and such functional groupings enable a consolidation strategy that minimizes undesirable epistatic effects.

As previously explained, the optimization of microbes for use in industrial fermentation is an important and difficult problem, with broad implications for the economy, society, and the natural world. Traditionally, microbial engineering has been performed through a slow and uncertain process of random mutagenesis. Such approaches leverage the natural evolutionary capacity of cells to adapt to artificially imposed selection pressure. Such approaches are also limited by the rarity of beneficial mutations, the ruggedness of the underlying fitness landscape, and more generally underutilize the state of the art in cellular and molecular biology.

Modern approaches leverage new understanding of cellular function at the mechanistic level and new molecular biology tools to perform targeted genetic manipulations to specific phenotypic ends. In practice, such rational approaches are confounded by the underlying complexity of biology. Causal mechanisms are poorly understood, particularly when attempting to combine two or more changes that each has an observed beneficial effect. Sometimes such consolidations of genetic changes yield positive outcomes (measured by increases in desired phenotypic activity), although the net positive outcome may be lower than expected and in some cases higher than expected. In other instances, such combinations produce either net neutral effect or a net negative effect. This phenomenon is referred to as epistasis, and is one of the fundamental challenges to microbial engineering (and genetic engineering generally).

As aforementioned, the present HTP genomic engineering platform solves many of the problems associated with traditional microbial engineering approaches. The present HTP platform uses automation technologies to perform hundreds or thousands of genetic mutations at once. In particular aspects, unlike the rational approaches described above, the disclosed HTP platform enables the parallel construction of thousands of mutants to more effectively explore large subsets of the relevant genomic space, as disclosed in U.S. application Ser. No. 15/140,296, entitled Microbial Strain Design System And Methods For Improved Large-Scale Production Of Engineered Nucleotide Sequences, incorporated by reference herein in its entirety. By trying “everything,” the present HTP platform sidesteps the difficulties induced by our limited biological understanding.

However, at the same time, the present HTP platform faces the problem of being fundamentally limited by the combinatorial explosive size of genomic space, and the effectiveness of computational techniques to interpret the generated data sets given the complexity of genetic interactions. Techniques are needed to explore subsets of vast combinatorial spaces in ways that maximize non-random selection of combinations that yield desired outcomes.

Somewhat similar HTP approaches have proved effective in the case of enzyme optimization. In this niche problem, a genomic sequence of interest (on the order of 1000 bases), encodes a protein chain with some complicated physical configuration. The precise configuration is determined by the collective electromagnetic interactions between its constituent atomic components. This combination of short genomic sequence and physically constrained folding problem lends itself specifically to greedy optimization strategies. That is, it is possible to individually mutate the sequence at every residue and shuffle the resulting mutants to effectively sample local sequence space at a resolution compatible with the Sequence Activity Response modeling.

However, for full genomic optimizations for biomolecules, such residue-centric approaches are insufficient for some important reasons. First, because of the exponential increase in relevant sequence space associated with genomic optimizations for biomolecules. Second, because of the added complexity of regulation, expression, and metabolic interactions in biomolecule synthesis. The present inventors have solved these problems via the taught epistasis mapping procedure.

The taught method for modeling epistatic interactions, between a collection of mutations for the purposes of more efficient and effective consolidation of said mutations into one or more genetic backgrounds, is groundbreaking and highly needed in the art.

When describing the epistasis mapping procedure, the terms “more efficient” and “more effective” refers to the avoidance of undesirable epistatic interactions among consolidation strains with respect to particular phenotypic objectives.

As the process has been generally elaborated upon above, a more specific workflow example will now be described.

First, one begins with a library of M mutations and one or more genetic backgrounds (e.g., parent bacterial strains). Neither the choice of library nor the choice of genetic backgrounds is specific to the method described here. But in a particular implementation, a library of mutations may include exclusively, or in combination: SNP swap libraries, Promoter swap libraries, or any other mutation library described herein.

In one implementation, only a single genetic background is provided. In this case, a collection of distinct genetic backgrounds (microbial mutants) will first be generated from this single background. This may be achieved by applying the primary library of mutations (or some subset thereof) to the given background for example, application of a HTP genetic design library of particular SNPs or a HTP genetic design library of particular promoters to the given genetic background, to create a population (perhaps 100's or 1,000's) of microbial mutants with an identical genetic background except for the particular genetic alteration from the given HTP genetic design library incorporated therein. As detailed below, this embodiment can lead to a combinatorial library or pairwise library.

In another implementation, a collection of distinct known genetic backgrounds may simply be given. As detailed below, this embodiment can lead to a subset of a combinatorial library.

In a particular implementation, the number of genetic backgrounds and genetic diversity between these backgrounds (measured in number of mutations or sequence edit distance or the like) is determined to maximize the effectiveness of this method.

A genetic background may be a natural, native or wild-type strain or a mutated, engineered strain. N distinct background strains may be represented by a vector b. In one example, the background b may represent engineered backgrounds formed by applying N primary mutations m₀=m₂, . . . m_(N)) to a wild-type background strain b₀ to form the N mutated background strains b=m₀ b₀=(m₁b₀, m₂b₀, . . . m_(N) b₀), where m_(i)b₀ represents the application of mutation m_(i) to background strain b₀.

In either case (i.e. a single provided genetic background or a collection of genetic backgrounds), the result is a collection of N genetically distinct backgrounds. Relevant phenotypes are measured for each background.

Second, each mutation in a collection of M mutations m₁ is applied to each background within the collection of N background strains b to form a collection of M×N mutants. In the implementation where the N backgrounds were themselves obtained by applying the primary set of mutations m₀ (as described above), the resulting set of mutants will sometimes be referred to as a combinatorial library or a pairwise library. In another implementation, in which a collection of known backgrounds has been provided explicitly, the resulting set of mutants may be referred to as a subset of a combinatorial library. Similar to generation of engineered background vectors, in embodiments, the input interface 202 receives the mutation vector mu and the background vector b, and a specified operation such as cross product.

Continuing with the engineered background example above, forming the M×N combinatorial library may be represented by the matrix formed by m₁×m₀ b₀, the cross product of m₁ applied to the N backgrounds of b=m₀ b₀, where each mutation in m₁ is applied to each background strain within b. Each ith row of the resulting M×N matrix represents the application of the ith mutation within m₁ to all the strains within background collection b. In one embodiment, m₁=m₀ and the matrix represents the pairwise application of the same mutations to starting strain b₀. In that case, the matrix is symmetric about its diagonal (M=N), and the diagonal may be ignored in any analysis since it represents the application of the same mutation twice.

In embodiments, forming the M×N matrix may be achieved by inputting into the input interface 202 the compound expression m₁×m₀b₀. The component vectors of the expression may be input directly with their elements explicitly specified, via one or more DNA specifications, or as calls to the library 206 to enable retrieval of the vectors during interpretation by interpreter 204. As described in U.S. patent application Ser. No. 15/140,296, entitled “Microbial Strain Design System and Methods for Improved Large Scale Production of Engineered Nucleotide Sequences,” via the interpreter 204, execution engine 207, order placement engine 208, and factory 210, the LIMS system 200 generates the microbial strains specified by the input expression.

Third, with reference to FIG. 42, the analysis equipment 214 measures phenotypic responses for each mutant within the M×N combinatorial library matrix (4202). As such, the collection of responses can be construed as an M×N Response Matrix R. Each element of R may be represented as r_(ij)=y(m_(i), m_(j)), where y represents the response (performance) of background strain b_(j) within engineered collection b as mutated by mutation m_(i). For simplicity, and practicality, we assume pairwise mutations where m₁=m₀. Where, as here, the set of mutations represents a pairwise mutation library, the resulting matrix may also be referred to as a gene interaction matrix or, more particularly, as a mutation interaction matrix.

Those skilled in the art will recognize that, in some embodiments, operations related to epistatic effects and predictive strain design may be performed entirely through automated means of the LIMS system 200, e.g., by the analysis equipment 214, or by human implementation, or through a combination of automated and manual means. When an operation is not fully automated, the elements of the LIMS system 200, e.g., analysis equipment 214, may, for example, receive the results of the human performance of the operations rather than generate results through its own operational capabilities. As described elsewhere herein, components of the LIMS system 200, such as the analysis equipment 214, may be implemented wholly or partially by one or more computer systems. In some embodiments, in particular where operations related to predictive strain design are performed by a combination of automated and manual means, the analysis equipment 214 may include not only computer hardware, software or firmware (or a combination thereof), but also equipment operated by a human operator such as that listed in Table 5 below, e.g., the equipment listed under the category of “Evaluate performance.”

Fourth, the analysis equipment 212 normalizes the response matrix. Normalization consists of a manual and/or, in this embodiment, automated processes of adjusting measured response values for the purpose of removing bias and/or isolating the relevant portions of the effect specific to this method. With respect to FIG. 42, the first step 4202 may include obtaining normalized measured data. In general, in the claims directed to predictive strain design and epistasis mapping, the terms “performance measure” or “measured performance” or the like may be used to describe a metric that reflects measured data, whether raw or processed in some manner, e.g., normalized data. In a particular implementation, normalization may be performed by subtracting a previously measured background response from the measured response value. In that implementation, the resulting response elements may be formed as r_(ij)=y(m_(i), m_(j))−y(m_(j)), where y(m_(j)) is the response of the engineered background strain b_(j) within engineered collection b caused by application of primary mutation m_(j) to parent strain b₀. Note that each row of the normalized response matrix is treated as a response profile for its corresponding mutation. That is, the ith row describes the relative effect of the corresponding mutation m_(i) applied to all the background strains b_(j) for j=1 to N.

With respect to the example of pairwise mutations, the combined performance/response of strains resulting from two mutations may be greater than, less than, or equal to the performance/response of the strain to each of the mutations individually. This effect is known as “epistasis,” and may, in some embodiments, be represented as e_(ij)=y(m_(i), m_(j))−(y(m_(i))+y(m_(j))). Variations of this mathematical representation are possible, and may depend upon, for example, how the individual changes biologically interact. As noted above, mutations from the same functional group are more likely to operate by the same mechanism, and are thus more likely to exhibit negative or neutral epistasis on overall host performance. In contrast, mutations from different functional groups are more likely to operate by independent mechanisms, which can lead to improved host performance by reducing redundant mutative effects, for example. Thus, mutations that yield dissimilar responses are more likely to combine in an additive manner than mutations that yield similar responses. This leads to the computation of similarity in the next step.

Fifth, the analysis equipment 214 measures the similarity among the responses—in the pairwise mutation example, the similarity between the effects of the ith mutation and jth (e.g., primary) mutation within the response matrix (4204). Recall that the ith row of R represents the performance effects of the ith mutation m_(i) on the N background strains, each of which may be itself the result of engineered mutations as described above. Thus, the similarity between the effects of the ith and jth mutations may be represented by the similarity s_(ij) between the ith and jth rows, ρ_(i) and ρ_(j), respectively, to form a similarity matrix S, an example of which is illustrated in FIG. 15. Similarity may be measured using many known techniques, such as cross-correlation or absolute cosine similarity, e.g., s_(ij)=abs(cos(ρ_(i), ρ_(j))).

As an alternative or supplement to a metric like cosine similarity, response profiles may be clustered to determine degree of similarity. Clustering may be performed by use of a distance-based clustering algorithms (e.g. k-mean, hierarchical agglomerative, etc.) in conjunction with suitable distance measure (e.g. Euclidean, Hamming, etc). Alternatively, clustering may be performed using similarity based clustering algorithms (e.g. spectral, min-cut, etc.) with a suitable similarity measure (e.g. cosine, correlation, etc). Of course, distance measures may be mapped to similarity measures and vice-versa via any number of standard functional operations (e.g., the exponential function). In one implementation, hierarchical agglomerative clustering may be used in conjunction absolute cosine similarity. (See FIG. 16A).

As an example of clustering, let C be a clustering of mutations m_(i) into k distinct clusters. Let C be the cluster membership matrix, where c_(ij) is the degree to which mutation i belongs to cluster j, a value between 0 and 1. The cluster-based similarity between mutations i and j is then given by C_(i)×C_(j) (the dot product of the ith and jth rows of C). In general, the cluster-based similarity matrix is given by CC^(T) (that is, C times C-transpose). In the case of hard-clustering (a mutation belongs to exactly one cluster), the similarity between two mutations is 1 if they belong to the same cluster and 0 if not.

As is described in Costanzo, The Genetic Landscape of a Cell, Science, Vol. 327, Issue 5964, Jan. 22, 2010, pp. 425-431 (incorporated by reference herein in its entirety), such a clustering of mutation response profiles relates to an approximate mapping of a cell's underlying functional organization. That is, mutations that cluster together tend to be related by an underlying biological process or metabolic pathway. Such mutations are referred to herein as a “functional group.” The key observation of this method is that if two mutations operate by the same biological process or pathway, then observed effects (and notably observed benefits) may be redundant. Conversely, if two mutations operate by distant mechanism, then it is less likely that beneficial effects will be redundant.

Sixth, based on the epistatic effect, the analysis equipment 214 selects pairs of mutations that lead to dissimilar responses, e.g., their cosine similarity metric falls below a similarity threshold, or their responses fall within sufficiently separated clusters, (e.g., in FIG. 15 and FIG. 16A) as shown in FIG. 42 (4206). Based on their dissimilarity, the selected pairs of mutations should consolidate into background strains better than similar pairs.

Based upon the selected pairs of mutations that lead to sufficiently dissimilar responses, the LIMS system (e.g., all of or some combination of interpreter 204, execution engine 207, order placer 208, and factory 210) may be used to design microbial strains having those selected mutations (4208). In embodiments, as described below and elsewhere herein, epistatic effects may be built into, or used in conjunction with the predictive model to weight or filter strain selection.

It is assumed that it is possible to estimate the performance (a.k.a. score) of a hypothetical strain obtained by consolidating a collection of mutations from the library into a particular background via some preferred predictive model. A representative predictive model utilized in the taught methods is provided in the below section entitled “Predictive Strain Design” that is found in the larger section of: “Computational Analysis and Prediction of Effects of Genome-Wide Genetic Design Criteria.”

When employing a predictive strain design technique such as linear regression, the analysis equipment 214 may restrict the model to mutations having low similarity measures by, e.g., filtering the regression results to keep only sufficiently dissimilar mutations. Alternatively, the predictive model may be weighted with the similarity matrix. For example, some embodiments may employ a weighted least squares regression using the similarity matrix to characterize the interdependencies of the proposed mutations. As an example, weighting may be performed by applying the “kernel” trick to the regression model. (To the extent that the “kernel trick” is general to many machine learning modeling approaches, this re-weighting strategy is not restricted to linear regression.)

Such methods are known to one skilled in the art. In embodiments, the kernel is a matrix having elements 1−w*s_(ij) where 1 is an element of the identity matrix, and w is a real value between 0 and 1. When w=0, this reduces to a standard regression model. In practice, the value of w will be tied to the accuracy (r² value or root mean square error (RMSE)) of the predictive model when evaluated against the pairwise combinatorial constructs and their associate effects y(m_(i), m_(j)). In one simple implementation, w is defined as w=1−r². In this case, when the model is fully predictive, w=1−r²=0 and consolidation is based solely on the predictive model and epistatic mapping procedure plays no role. On the other hand, when the predictive model is not predictive at all, w=1−r²=1 and consolidation is based solely on the epistatic mapping procedure. During each iteration, the accuracy can be assessed to determine whether model performance is improving.

It should be clear that the epistatic mapping procedure described herein does not depend on which model is used by the analysis equipment 214. Given such a predictive model, it is possible to score and rank all hypothetical strains accessible to the mutation library via combinatorial consolidation.

In some embodiments, to account for epistatic effects, the dissimilar mutation response profiles may be used by the analysis equipment 214 to augment the score and rank associated with each hypothetical strain from the predictive model. This procedure may be thought of broadly as a re-weighting of scores, so as to favor candidate strains with dissimilar response profiles (e.g., strains drawn from a diversity of clusters). In one simple implementation, a strain may have its score reduced by the number of constituent mutations that do not satisfy the dissimilarity threshold or that are drawn from the same cluster (with suitable weighting). In a particular implementation, a hypothetical strain's performance estimate may be reduced by the sum of terms in the similarity matrix associated with all pairs of constituent mutations associated with the hypothetical strain (again with suitable weighting). Hypothetical strains may be re-ranked using these augmented scores. In practice, such re-weighting calculations may be performed in conjunction with the initial scoring estimation.

The result is a collection of hypothetical strains with score and rank augmented to more effectively avoid confounding epistatic interactions. Hypothetical strains may be constructed at this time, or they may be passed to another computational method for subsequent analysis or use.

Those skilled in the art will recognize that epistasis mapping and iterative predictive strain design as described herein are not limited to employing only pairwise mutations, but may be expanded to the simultaneous application of many more mutations to a background strain. In another embodiment, additional mutations may be applied sequentially to strains that have already been mutated using mutations selected according to the predictive methods described herein. In another embodiment, epistatic effects are imputed by applying the same genetic mutation to a number of strain backgrounds that differ slightly from each other, and noting any significant differences in positive response profiles among the modified strain backgrounds.

Organisms Amenable to Genetic Design

The disclosed HTP genomic engineering platform is exemplified with industrial microbial cell cultures (e.g., Corynebacterium and A. niger), but is applicable to any host cell organism where desired traits can be identified in a population of genetic mutants.

Thus, as used herein, the term “microorganism” should be taken broadly. It includes, but is not limited to, the two prokaryotic domains, Bacteria and Archaea, as well as certain eukaryotic fungi and protists. However, in certain aspects, “higher” eukaryotic organisms such as insects, plants, and animals can be utilized in the methods taught herein.

The present disclosure provides working examples for both prokaryotic (Examples 1-9) and eukaryotic (Example 10-11) host cells

Suitable host cells include, but are not limited to: bacterial cells, algal cells, plant cells, fungal cells, insect cells, and mammalian cells. In one illustrative embodiment, suitable host cells include E. coli (e.g., SHuffle™ competent E. coli available from New England BioLabs in Ipswich, Mass.).

Other suitable host organisms of the present disclosure include microorganisms of the genus Corynebacterium. In some embodiments, preferred Corynebacterium strains/species include: C. efficiens, with the deposited type strain being DSM44549, C. glutamicum, with the deposited type strain being ATCC13032, and C. ammoniagenes, with the deposited type strain being ATCC6871. In some embodiments the preferred host of the present disclosure is C. glutamicum.

Suitable host strains of the genus Corynebacterium, in particular of the species Corynebacterium glutamicum, are in particular the known wild-type strains: Corynebacterium glutamicum ATCC13032, Corynebacterium acetoglutamicum ATCC15806, Corynebacterium acetoacidophilum ATCC13870, Corynebacterium melassecola ATCC 17965, Corynebacterium thermoaminogenes FERM BP-1539, Brevibacterium flavum ATCC14067, Brevibacterium lactofermentum ATCC13869, and Brevibacterium divaricatum ATCC14020; and L-amino acid-producing mutants, or strains, prepared therefrom, such as, for example, the L-lysine-producing strains: Corynebacterium glutamicum FERM-P 1709, Brevibacterium flavum FERM-P 1708, Brevibacterium lactofermentum FERM-P 1712, Corynebacterium glutamicum FERM-P 6463, Corynebacterium glutamicum FERM-P 6464, Corynebacterium glutamicum DM58-1, Corynebacterium glutamicum DG52-5, Corynebacterium glutamicum DSM5714, and Corynebacterium glutamicum DSM12866.

The term “Micrococcus glutamicus” has also been in use for C. glutamicum. Some representatives of the species C. efficiens have also been referred to as C. thermoaminogenes in the prior art, such as the strain FERM BP-1539, for example.

In some embodiments, the host cell of the present disclosure is a eukaryotic cell. Suitable eukaryotic host cells include, but are not limited to: fungal cells, algal cells, insect cells, animal cells, and plant cells. Suitable fungal host cells include, but are not limited to: Ascomycota, Basidiomycota, Deuteromycota, Zygomycota, Fungi imperfecti. Certain preferred fungal host cells include yeast cells and filamentous fungal cells. Suitable filamentous fungi host cells include, for example, any filamentous forms of the subdivision Eumycotina and Oomycota. (see, e.g., Hawksworth et al., In Ainsworth and Bisby's Dictionary of The Fungi, 8th edition, 1995, CAB International, University Press, Cambridge, UK, which is incorporated herein by reference). Filamentous fungi are characterized by a vegetative mycelium with a cell wall composed of chitin, cellulose and other complex polysaccharides. The filamentous fungi host cells are morphologically distinct from yeast.

In certain illustrative, but non-limiting embodiments, the filamentous fungal host cell may be a cell of a species of: Achlya, Acremonium, Aspergillus, Aureobasidium, Bjerkandera, Ceriporiopsis, Cephalosporium, Chrysosporium, Cochliobolus, Corynascus, Cryphonectria, Cryptococcus, Coprinus, Coriolus, Diplodia, Endothis, Fusarium, Gibberella, Gliocladium, Humicola, Hypocrea, Myceliophthora (e.g., Myceliophthora thermophila), Mucor, Neurospora, Penicillium, Podospora, Phlebia, Piromyces, Pyricularia, Rhizomucor, Rhizopus, Schizophyllum, Scytalidium, Sporotrichum, Talaromyces, Thermoascus, Thielavia, Tramates, Tolypocladium, Trichoderma, Verticillium, Volvariella, or teleomorphs, or anamorphs, and synonyms or taxonomic equivalents thereof. In one embodiment, the filamentous fungus is selected from the group consisting of A. nidulans, A. oryzae, A. sojae, and Aspergilli of the A. niger Group. In an embodiment, the filamentous fungus is Aspergillus niger.

In another embodiment, specific mutants of the fungal species are used for the methods and systems provided herein. In one embodiment, specific mutants of the fungal species are used which are suitable for the high-throughput and/or automated methods and systems provided herein. Examples of such mutants can be strains that protoplast very well; strains that produce mainly or, more preferably, only protoplasts with a single nucleus; strains that regenerate efficiently in microtiter plates, strains that regenerate faster and/or strains that take up polynucleotide (e.g., DNA) molecules efficiently, strains that produce cultures of low viscosity such as, for example, cells that produce hyphae in culture that are not so entangled as to prevent isolation of single clones and/or raise the viscosity of the culture, strains that have reduced random integration (e.g., disabled non-homologous end joining pathway) or combinations thereof.

In yet another embodiment, a specific mutant strain for use in the methods and systems provided herein can be strains lacking a selectable marker gene such as, for example, uridine-requiring mutant strains. These mutant strains can be either deficient in orotidine 5 phosphate decarboxylase (OMPD) or orotate p-ribosyl transferase (OPRT) encoded by the pyrG or pyrE gene, respectively (T. Goosen et al., Curr Genet. 1987, 11:499 503; J. Begueret et al., Gene. 1984 32:487 92.

In one embodiment, specific mutant strains for use in the methods and systems provided herein are strains that possess a compact cellular morphology characterized by shorter hyphae and a more yeast-like appearance.

Suitable yeast host cells include, but are not limited to: Candida, Hansenula, Saccharomyces, Schizosaccharomyces, Pichia, Kluyveromyces, and Yarrowia. In some embodiments, the yeast cell is Hansenula polymorpha, Saccharomyces cerevisiae, Saccaromyces carlsbergensis, Saccharomyces diastaticus, Saccharomyces norbensis, Saccharomyces kluyveri, Schizosaccharomyces pombe, Pichia pastoris, Pichia finlandica, Pichia trehalophila, Pichia kodamae, Pichia membranaefaciens, Pichia opuntiae, Pichia thermotolerans, Pichia salictaria, Pichia quercuum, Pichia pijperi, Pichia stipitis, Pichia methanolica, Pichia angusta, Kluyveromyces lactis, Candida albicans, or Yarrowia lipolytica.

In certain embodiments, the host cell is an algal cell such as, Chlamydomonas (e.g., C. Reinhardtii) and Phormidium (P. sp. ATCC29409).

In other embodiments, the host cell is a prokaryotic cell. Suitable prokaryotic cells include gram positive, gram negative, and gram-variable bacterial cells. The host cell may be a species of, but not limited to: Agrobacterium, Alicyclobacillus, Anabaena, Anacystis, Acinetobacter, Acidothermus, Arthrobacter, Azobacter, Bacillus, Bifidobacterium, Brevibacterium, Butyrivibrio, Buchnera, Campestris, Camplyobacter, Clostridium, Corynebacterium, Chromatium, Coprococcus, Escherichia, Enterococcus, Enterobacter, Erwinia, Fusobacterium, Faecalibacterium, Francisella, Flavobacterium, Geobacillus, Haemophilus, Helicobacter, Klebsiella, Lactobacillus, Lactococcus, Ilyobacter, Micrococcus, Microbacterium, Mesorhizobium, Methylobacterium, Methylobacterium, Mycobacterium, Neisseria, Pantoea, Pseudomonas, Prochlorococcus, Rhodobacter, Rhodopseudomonas, Rhodopseudomonas, Roseburia, Rhodospirillum, Rhodococcus, Scenedesmus, Streptomyces, Streptococcus, Synecoccus, Saccharomonospora, Saccharopolyspora, Staphylococcus, Serratia, Salmonella, Shigella, Thermoanaerobacterium, Tropheryma, Tularensis, Temecula, Thermosynechococcus, Thermococcus, Ureaplasma, Xanthomonas, Xylella, Yersinia, and Zymomonas. In some embodiments, the host cell is Corynebacterium glutamicum.

In some embodiments, the bacterial host strain is an industrial strain. Numerous bacterial industrial strains are known and suitable in the methods and compositions described herein.

In some embodiments, the bacterial host cell is of the Agrobacterium species (e.g., A. radiobacter, A. rhizogenes, A. rubi), the Arthrobacter species (e.g., A. aurescens, A. citreus, A. globformis, A. hydrocarboglutamicus, A. mysorens, A. nicotianae, A. paraffineus, A. protophonniae, A. roseoparaffinus, A. sulfureus, A. ureafaciens), the Bacillus species (e.g., B. thuringiensis, B. anthracis, B. megaterium, B. subtilis, B. lentus, B. circulars, B. pumilus, B. lautus, B. coagulans, B. brevis, B. firmus, B. alkaophius, B. licheniformis, B. clausii, B. stearothermophilus, B. halodurans and B. amyloliquefaciens. In particular embodiments, the host cell will be an industrial Bacillus strain including but not limited to B. subtilis, B. pumilus, B. licheniformis, B. megaterium, B. clausii, B. stearothermophilus and B. amyloliquefaciens. In some embodiments, the host cell will be an industrial Clostridium species (e.g., C. acetobutylicum, C. tetani E88, C. lituseburense, C. saccharobutylicum, C. perfringens, C. beijerinckii). In some embodiments, the host cell will be an industrial Corynebacterium species (e.g., C. glutamicum, C. acetoacidophilum). In some embodiments, the host cell will be an industrial Escherichia species (e.g., E. coli). In some embodiments, the host cell will be an industrial Erwinia species (e.g., E. uredovora, E. carotovora, E. ananas, E. herbicola, E. punctata, E. terreus). In some embodiments, the host cell will be an industrial Pantoea species (e.g., P. citrea, P. agglomerans). In some embodiments, the host cell will be an industrial Pseudomonas species, (e.g., P. putida, P. aeruginosa, P. mevalonii). In some embodiments, the host cell will be an industrial Streptococcus species (e.g., S. equisimiles, S. pyogenes, S. uberis). In some embodiments, the host cell will be an industrial Streptomyces species (e.g., S. ambofaciens, S. achromogenes, S. avermitilis, S. coelicolor, S. aureofaciens, S. aureus, S. fungicidicus, S. griseus, S. lividans). In some embodiments, the host cell will be an industrial Zymomonas species (e.g., Z. mobilis, Z. lipolytica), and the like.

The present disclosure is also suitable for use with a variety of animal cell types, including mammalian cells, for example, human (including 293, WI38, PER.C6 and Bowes melanoma cells), mouse (including 3T3, NS0, NS1, Sp2/0), hamster (CHO, BHK), monkey (COS, FRhL, Vero), and hybridoma cell lines.

In various embodiments, strains that may be used in the practice of the disclosure including both prokaryotic and eukaryotic strains, are readily accessible to the public from a number of culture collections such as American Type Culture Collection (ATCC), Deutsche Sammlung von Mikroorganismen and Zellkulturen GmbH (DSM), Centraalbureau Voor Schimmelcultures (CBS), and Agricultural Research Service Patent Culture Collection, Northern Regional Research Center (NRRL).

In some embodiments, the methods of the present disclosure are also applicable to multi-cellular organisms. For example, the platform could be used for improving the performance of crops. The organisms can comprise a plurality of plants such as Gramineae, Fetucoideae, Poacoideae, Agrostis, Phleum, Dactylis, Sorgum, Setaria, Zea, Oryza, Triticum, Secale, Avena, Hordeum, Saccharum, Poa, Festuca, Stenotaphrum, Cynodon, Coix, Olyreae, Phareae, Compositae or Leguminosae. For example, the plants can be corn, rice, soybean, cotton, wheat, rye, oats, barley, pea, beans, lentil, peanut, yam bean, cowpeas, velvet beans, clover, alfalfa, lupine, vetch, lotus, sweet clover, wisteria, sweet pea, sorghum, millet, sunflower, canola or the like. Similarly, the organisms can include a plurality of animals such as non-human mammals, fish, insects, or the like.

Generating Genetic Diversity Pools for Utilization in the Genetic Design & HTP Microbial Engineering Platform

In some embodiments, the methods of the present disclosure are characterized as genetic design. As used herein, the term genetic design refers to the reconstruction or alteration of a host organism's genome through the identification and selection of the most optimum variants of a particular gene, portion of a gene, promoter, stop codon, 5′UTR, 3′UTR, or other DNA sequence to design and create new superior host cells.

In some embodiments, a first step in the genetic design methods of the present disclosure is to obtain an initial genetic diversity pool population with a plurality of sequence variations from which a new host genome may be reconstructed.

In some embodiments, a subsequent step in the genetic design methods taught herein is to use one or more of the aforementioned HTP molecular tool sets (e.g. SNP swapping or promoter swapping) to construct HTP genetic design libraries, which then function as drivers of the genomic engineering process, by providing libraries of particular genomic alterations for testing in a host cell.

Harnessing Diversity Pools from Existing Wild-Type Strains

In some embodiments, the present disclosure teaches methods for identifying the sequence diversity present among microbes of a given wild-type population. Therefore, a diversity pool can be a given number n of wild-type microbes utilized for analysis, with said microbes' genomes representing the “diversity pool.”

In some embodiments, the diversity pools can be the result of existing diversity present in the natural genetic variation among said wild-type microbes. This variation may result from strain variants of a given host cell or may be the result of the microbes being different species entirely. Genetic variations can include any differences in the genetic sequence of the strains, whether naturally occurring or not. In some embodiments, genetic variations can include SNPs swaps, PRO swaps, Start/Stop Codon swaps, or STOP swaps, among others.

Harnessing Diversity Pools from Existing Industrial Strain Variants

In other embodiments of the present disclosure, diversity pools are strain variants created during traditional strain improvement processes (e.g., one or more host organism strains generated via random mutation and selected for improved yields over the years). Thus, in some embodiments, the diversity pool or host organisms can comprise a collection of historical production strains.

In particular aspects, a diversity pool may be an original parent microbial strain (S₁) with a “baseline” genetic sequence at a particular time point (S₁Gen₁) and then any number of subsequent offspring strains (S₂, S₃, S₄, S₅, etc., generalizable to S_(2-n)) that were derived/developed from said S₁ strain and that have a different genome (S_(2-n)Gen_(2-n)), in relation to the baseline genome of S₁.

For example, in some embodiments, the present disclosure teaches sequencing the microbial genomes in a diversity pool to identify the SNP's present in each strain. In one embodiment, the strains of the diversity pool are historical microbial production strains. Thus, a diversity pool of the present disclosure can include for example, an industrial base strain, and one or more mutated industrial strains produced via traditional strain improvement programs.

Once all SNPs in the diversity pool are identified, the present disclosure teaches methods of SNP swapping and screening methods to delineate (i.e. quantify and characterize) the effects (e.g. creation of a phenotype of interest) of SNPs individually and in groups. Thus, as aforementioned, an initial step in the taught platform can be to obtain an initial genetic diversity pool population with a plurality of sequence variations, e.g. SNPs. Then, a subsequent step in the taught platform can be to use one or more of the aforementioned HTP molecular tool sets (e.g. SNP swapping) to construct HTP genetic design libraries, which then function as drivers of the genomic engineering process, by providing libraries of particular genomic alterations for testing in a microbe.

In some embodiments, the SNP swapping methods of the present disclosure comprise the step of introducing one or more SNPs identified in a mutated strain (e.g., a strain from amongst S_(2-n)Gen_(2-n)) to a base strain (S₁Gen₁) or wild-type strain.

In other embodiments, the SNP swapping methods of the present disclosure comprise the step of removing one or more SNPs identified in a mutated strain (e.g., a strain from amongst S_(2-n)Gen_(2-n)).

Creating Diversity Pools Via Mutagenesis

In some embodiments, the mutations of interest in a given diversity pool population of cells can be artificially generated by any means for mutating strains, including mutagenic chemicals, or radiation. The term “mutagenizing” is used herein to refer to a method for inducing one or more genetic modifications in cellular nucleic acid material.

The term “genetic modification” refers to any alteration of DNA. Representative gene modifications include nucleotide insertions, deletions, substitutions, and combinations thereof, and can be as small as a single base or as large as tens of thousands of bases. Thus, the term “genetic modification” encompasses inversions of a nucleotide sequence and other chromosomal rearrangements, whereby the position or orientation of DNA comprising a region of a chromosome is altered. A chromosomal rearrangement can comprise an intrachromosomal rearrangement or an interchromosomal rearrangement.

In one embodiment, the mutagenizing methods employed in the presently claimed subject matter are substantially random such that a genetic modification can occur at any available nucleotide position within the nucleic acid material to be mutagenized. Stated another way, in one embodiment, the mutagenizing does not show a preference or increased frequency of occurrence at particular nucleotide sequences.

The methods of the disclosure can employ any mutagenic agent including, but not limited to: ultraviolet light, X-ray radiation, gamma radiation, N-ethyl-N-nitrosourea (ENU), methyinitrosourea (MNU), procarbazine (PRC), triethylene melamine (TEM), acrylamide monomer (AA), chlorambucil (CHL), melphalan (MLP), cyclophosphamide (CPP), diethyl sulfate (DES), ethyl methane sulfonate (EMS), methyl methane sulfonate (MMS), 6-mercaptopurine (6-MP), mitomycin-C(MMC), N-methyl-N′-nitro-N-nitrosoguanidine (MNNG), ³H₂O, and urethane (UR) (See e.g., Rinchik, 1991; Marker et al., 1997; and Russell, 1990). Additional mutagenic agents are well known to persons having skill in the art, including those described in http://www.iephb.nw.ru/˜spirov/hazard/mutagen_1st. html.

The term “mutagenizing” also encompasses a method for altering (e.g., by targeted mutation) or modulating a cell function, to thereby enhance a rate, quality, or extent of mutagenesis. For example, a cell can be altered or modulated to thereby be dysfunctional or deficient in DNA repair, mutagen metabolism, mutagen sensitivity, genomic stability, or combinations thereof. Thus, disruption of gene functions that normally maintain genomic stability can be used to enhance mutagenesis. Representative targets of disruption include, but are not limited to DNA ligase I (Bentley et al., 2002) and casein kinase I (U.S. Pat. No. 6,060,296).

In some embodiments, site-specific mutagenesis (e.g., primer-directed mutagenesis using a commercially available kit such as the Transformer Site Directed mutagenesis kit (Clontech)) is used to make a plurality of changes throughout a nucleic acid sequence in order to generate nucleic acid encoding a cleavage enzyme of the present disclosure.

The frequency of genetic modification upon exposure to one or more mutagenic agents can be modulated by varying dose and/or repetition of treatment, and can be tailored for a particular application.

Thus, in some embodiments, “mutagenesis” as used herein comprises all techniques known in the art for inducing mutations, including error-prone PCR mutagenesis, oligonucleotide-directed mutagenesis, site-directed mutagenesis, and iterative sequence recombination by any of the techniques described herein.

Single Locus Mutations to Generate Diversity

In some embodiments, the present disclosure teaches mutating cell populations by introducing, deleting, or replacing selected portions of genomic DNA. Thus, in some embodiments, the present disclosure teaches methods for targeting mutations to a specific locus. In other embodiments, the present disclosure teaches the use of gene editing technologies such as ZFNs, TALENS, or CRISPR, to selectively edit target DNA regions.

In other embodiments, the present disclosure teaches mutating selected DNA regions outside of the host organism, and then inserting the mutated sequence back into the host organism. For example, in some embodiments, the present disclosure teaches mutating native or synthetic promoters to produce a range of promoter variants with various expression properties (see promoter ladder infra). In other embodiments, the present disclosure is compatible with single gene optimization techniques, such as ProSAR (Fox et al. 2007. “Improving catalytic function by ProSAR-driven enzyme evolution.” Nature Biotechnology Vol 25 (3) 338-343, incorporated by reference herein).

In some embodiments, the selected regions of DNA are produced in vitro via gene shuffling of natural variants, or shuffling with synthetic oligos, plasmid-plasmid recombination, virus plasmid recombination, virus-virus recombination. In other embodiments, the genomic regions are produced via error-prone PCR (see e.g., FIG. 1).

In some embodiments, generating mutations in selected genetic regions is accomplished by “reassembly PCR.” Briefly, oligonucleotide primers (oligos) are synthesized for PCR amplification of segments of a nucleic acid sequence of interest, such that the sequences of the oligonucleotides overlap the junctions of two segments. The overlap region is typically about 10 to 100 nucleotides in length. Each of the segments is amplified with a set of such primers. The PCR products are then “reassembled” according to assembly protocols. In brief, in an assembly protocol, the PCR products are first purified away from the primers, by, for example, gel electrophoresis or size exclusion chromatography. Purified products are mixed together and subjected to about 1-10 cycles of denaturing, reannealing, and extension in the presence of polymerase and deoxynucleoside triphosphates (dNTP's) and appropriate buffer salts in the absence of additional primers (“self-priming”). Subsequent PCR with primers flanking the gene are used to amplify the yield of the fully reassembled and shuffled genes.

In some embodiments of the disclosure, mutated DNA regions, such as those discussed above, are enriched for mutant sequences so that the multiple mutant spectrum, i.e. possible combinations of mutations, is more efficiently sampled. In some embodiments, mutated sequences are identified via a mutS protein affinity matrix (Wagner et al., Nucleic Acids Res. 23(19):3944-3948 (1995); Su et al., Proc. Natl. Acad. Sci. (U.S.A.), 83:5057-5061(1986)) with a preferred step of amplifying the affinity-purified material in vitro prior to an assembly reaction. This amplified material is then put into an assembly or reassembly PCR reaction as described in later portions of this application.

Promoter Ladders

Promoters regulate the rate at which genes are transcribed and can influence transcription in a variety of ways. Constitutive promoters, for example, direct the transcription of their associated genes at a constant rate regardless of the internal or external cellular conditions, while regulatable promoters increase or decrease the rate at which a gene is transcribed depending on the internal and/or the external cellular conditions, e.g. growth rate, temperature, responses to specific environmental chemicals, and the like. Promoters can be isolated from their normal cellular contexts and engineered to regulate the expression of virtually any gene, enabling the effective modification of cellular growth, product yield and/or other phenotypes of interest.

In some embodiments, the present disclosure teaches methods for producing promoter ladder libraries for use in downstream genetic design methods. For example, in some embodiments, the present disclosure teaches methods of identifying one or more promoters and/or generating variants of one or more promoters within a host cell, which exhibit a range of expression strengths, or superior regulatory properties. A particular combination of these identified and/or generated promoters can be grouped together as a promoter ladder, which is explained in more detail below.

In some embodiments, the present disclosure teaches the use of promoter ladders. In some embodiments, the promoter ladders of the present disclosure comprise promoters exhibiting a continuous range of expression profiles. For example, in some embodiments, promoter ladders are created by: identifying natural, native, or wild-type promoters that exhibit a range of expression strengths in response to a stimuli, or through constitutive expression (see e.g., FIG. 20 and FIGS. 28-30). These identified promoters can be grouped together as a promoter ladder.

In other embodiments, the present disclosure teaches the creation of promoter ladders exhibiting a range of expression profiles across different conditions. For example, in some embodiments, the present disclosure teaches creating a ladder of promoters with expression peaks spread throughout the different stages of a fermentation (see e.g., FIG. 28). In other embodiments, the present disclosure teaches creating a ladder of promoters with different expression peak dynamics in response to a specific stimulus (see e.g., FIG. 29). Persons skilled in the art will recognize that the regulatory promoter ladders of the present disclosure can be representative of any one or more regulatory profiles.

In some embodiments, the promoter ladders of the present disclosure are designed to perturb gene expression in a predictable manner across a continuous range of responses. In some embodiments, the continuous nature of a promoter ladder confers strain improvement programs with additional predictive power. For example, in some embodiments, swapping promoters or termination sequences of a selected metabolic pathway can produce a host cell performance curve, which identifies the most optimum expression ratio or profile; producing a strain in which the targeted gene is no longer a limiting factor for a particular reaction or genetic cascade, while also avoiding unnecessary over expression or misexpression under inappropriate circumstances. In some embodiments, promoter ladders are created by: identifying natural, native, or wild-type promoters exhibiting the desired profiles. In other embodiments, the promoter ladders are created by mutating naturally occurring promoters to derive multiple mutated promoter sequences. Each of these mutated promoters is tested for effect on target gene expression. In some embodiments, the edited promoters are tested for expression activity across a variety of conditions, such that each promoter variant's activity is documented/characterized/annotated and stored in a database. The resulting edited promoter variants are subsequently organized into promoter ladders arranged based on the strength of their expression (e.g., with highly expressing variants near the top, and attenuated expression near the bottom, therefore leading to the term “ladder”).

In some embodiments, the present disclosure teaches promoter ladders that are a combination of identified naturally occurring promoters and mutated variant promoters.

In some embodiments, the present disclosure teaches methods of identifying natural, native, or wild-type promoters that satisfied both of the following criteria: 1) represented a ladder of constitutive promoters; and 2) could be encoded by short DNA sequences, ideally less than 100 base pairs. In some embodiments, constitutive promoters of the present disclosure exhibit constant gene expression across two selected growth conditions (typically compared among conditions experienced during industrial cultivation). In some embodiments, the promoters of the present disclosure will consist of a ˜60 base pair core promoter, and a 5′ UTR between 26- and 40 base pairs in length.

In some embodiments, one or more of the aforementioned identified naturally occurring promoter sequences are chosen for gene editing. In some embodiments, the natural promoters are edited via any of the mutation methods described supra. In other embodiments, the promoters of the present disclosure are edited by synthesizing new promoter variants with the desired sequence.

The entire disclosure of U.S. Patent Application No. 62/264,232, filed on Dec. 7, 2015, is hereby incorporated by reference in its entirety for all purposes

A non-exhaustive list of the promoters of the present disclosure is provided in the below Table 1. Each of the promoter sequences can be referred to as a heterologous promoter or heterologous promoter polynucleotide.

TABLE 1 Selected promoter sequences of the present disclosure. SEQ ID Promoter Short No. Name Promoter Name 1 P1 Pcg0007_lib_39 2 P2 Pcg0007 3 P3 Pcg1860 4 P4 Pcg0755 5 P5 Pcg0007_265 6 P6 Pcg3381 7 P7 Pcg0007_119 8 P8 Pcg3121

In some embodiments, the promoters of the present disclosure exhibit at least 100%, 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81%, 80%, 79%, 78%, 77%, 76%, or 75% sequence identity with a promoter from the above table.

Terminator Ladders

In some embodiments, the present disclosure teaches methods of improving genetically engineered host strains by providing one or more transcriptional termination sequences at a position 3′ to the end of the RNA encoding element. In some embodiments, the present disclosure teaches that the addition of termination sequences improves the efficiency of RNA transcription of a selected gene in the genetically engineered host. In other embodiments, the present disclosure teaches that the addition of termination sequences reduces the efficiency of RNA transcription of a selected gene in the genetically engineered host. Thus in some embodiments, the terminator ladders of the present disclosure comprises a series of terminator sequences exhibiting a range of transcription efficiencies (e.g., one weak terminator, one average terminator, and one strong promoter).

A transcriptional termination sequence may be any nucleotide sequence, which when placed transcriptionally downstream of a nucleotide sequence encoding an open reading frame, causes the end of transcription of the open reading frame. Such sequences are known in the art and may be of prokaryotic, eukaryotic or phage origin. Examples of terminator sequences include, but are not limited to, PTH-terminator, pET-T7 terminator, T3-T_(φ) terminator, pBR322-P4 terminator, vesicular stomatitus virus terminator, rrnB-T₁ terminator, rrnC terminator, TTadc transcriptional terminator, and yeast-recognized termination sequences, such as Matα (α-factor) transcription terminator, native α-factor transcription termination sequence, ADR1transcription termination sequence, ADH2transcription termination sequence, and GAPD transcription termination sequence. A non-exhaustive listing of transcriptional terminator sequences may be found in the iGEM registry, which is available at: http://partsregistry.org/Terminators/Catalog.

In some embodiments, transcriptional termination sequences may be polymerase-specific or nonspecific, however, transcriptional terminators selected for use in the present embodiments should form a ‘functional combination’ with the selected promoter, meaning that the terminator sequence should be capable of terminating transcription by the type of RNA polymerase initiating at the promoter. For example, in some embodiments, the present disclosure teaches a eukaryotic RNA pol II promoter and eukaryotic RNA pol II terminators, a T7 promoter and T7 terminators, a T3 promoter and T3 terminators, a yeast-recognized promoter and yeast-recognized termination sequences, etc., would generally form a functional combination. The identity of the transcriptional termination sequences used may also be selected based on the efficiency with which transcription is terminated from a given promoter. For example, a heterologous transcriptional terminator sequence may be provided transcriptionally downstream of the RNA encoding element to achieve a termination efficiency of at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% from a given promoter.

In some embodiments, efficiency of RNA transcription from the engineered expression construct can be improved by providing nucleic acid sequence forms a secondary structure comprising two or more hairpins at a position 3′ to the end of the RNA encoding element. Not wishing to be bound by a particular theory, the secondary structure destabilizes the transcription elongation complex and leads to the polymerase becoming dissociated from the DNA template, thereby minimizing unproductive transcription of non-functional sequence and increasing transcription of the desired RNA. Accordingly, a termination sequence may be provided that forms a secondary structure comprising two or more adjacent hairpins. Generally, a hairpin can be formed by a palindromic nucleotide sequence that can fold back on itself to form a paired stem region whose arms are connected by a single stranded loop. In some embodiments, the termination sequence comprises 2, 3, 4, 5, 6, 7, 8, 9, 10 or more adjacent hairpins. In some embodiments, the adjacent hairpins are separated by 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 unpaired nucleotides. In some embodiments, a hairpin stem comprises 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more base pairs in length. In certain embodiments, a hairpin stem is 12 to 30 base pairs in length. In certain embodiments, the termination sequence comprises two or more medium-sized hairpins having stem region comprising about 9 to 25 base pairs. In some embodiments, the hairpin comprises a loop-forming region of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides. In some embodiments, the loop-forming region comprises 4-8 nucleotides. Not wishing to be bound by a particular theory, stability of the secondary structure can be correlated with termination efficiency. Hairpin stability is determined by its length, the number of mismatches or bulges it contains and the base composition of the paired region. Pairings between guanine and cytosine have three hydrogen bonds and are more stable compared to adenine-thymine pairings, which have only two. The G/C content of a hairpin-forming palindromic nucleotide sequence can be at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90% or more. In some embodiments, the G/C content of a hairpin-forming palindromic nucleotide sequence is at least 80%. In some embodiments, the termination sequence is derived from one or more transcriptional terminator sequences of prokaryotic, eukaryotic or phage origin. In some embodiments, a nucleotide sequence encoding a series of 4, 5, 6, 7, 8, 9, 10 or more adenines (A) are provided 3′ to the termination sequence.

In some embodiments, the present disclosure teaches the use of a series of tandem termination sequences. In some embodiments, the first transcriptional terminator sequence of a series of 2, 3, 4, 5, 6, 7, or more may be placed directly 3′ to the final nucleotide of the dsRNA encoding element or at a distance of at least 1-5, 5-10, 10-15, 15-20, 20-25, 25-30, 30-35, 35-40, 40-45, 45-50, 50-100, 100-150, 150-200, 200-300, 300-400, 400-500, 500-1,000 or more nucleotides 3′ to the final nucleotide of the dsRNA encoding element. The number of nucleotides between tandem transcriptional terminator sequences may be varied, for example, transcriptional terminator sequences may be separated by 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 10-15, 15-20, 20-25, 25-30, 30-35, 35-40, 40-45, 45-50 or more nucleotides. In some embodiments, the transcriptional terminator sequences may be selected based on their predicted secondary structure as determined by a structure prediction algorithm. Structural prediction programs are well known in the art and include, for example, CLC Main Workbench.

Persons having skill in the art will recognize that the methods of the present disclosure are compatible with any termination sequence. In some embodiments, the present disclosure teaches use of annotated Corynebacterium glutamicum terminators as disclosed in from Pfeifer-Sancar et al. 2013. “Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique” Pfeifer-Sancar et al. BMC Genomics 2013, 14:888). In other embodiments, the present disclosure teaches use of transcriptional terminator sequences found in the iGEM registry, which is available at: http://partsregistry.org/Terminators/Catalog. A non-exhaustive listing of transcriptional terminator sequences of the present disclosure is provided in Table 1.1 below.

TABLE 1.1 Non-exhaustive list of termination sequences of the present disclosure. E. coli Name Description Direction Length BBa_B0010 T1 from E. coli rrnB Forward 80 BBa_B0012 TE from coliphageT7 Forward 41 BBa_B0013 TE from coliphage T7 (+/−) Forward 47 BBa_B0015 double terminator (B0010-B0012) Forward 129 BBa_B0017 double terminator (B0010-B0010) Forward 168 BBa_B0053 Terminator (His) Forward 72 BBa_B0055 -- No description -- 78 BBa_B1002 Terminator (artificial, Forward 34 small, % T~= 85%) BBa_B1003 Terminator (artificial, small, % T~= 80) Forward 34 BBa_B1004 Terminator (artificial, small, % T~= 55) Forward 34 BBa_B1005 Terminator (artificial, Forward 34 small, % T~= 25% BBa_B1006 Terminator (artificial, large, % T~>90) Forward 39 BBa_B1010 Terninator (artificial, large, % T~<10) Forward 40 BBa_I11013 Modification of biobricks part 129 BBa_B0015 BBa_I51003 -- No description -- 110 BBa_J61048 [rnpB-T1] Terminator Forward 113 BBa_K1392970 Terminator + Tetr Promoter + T4 623 Endolysin BBa_K1486001 Arabinose promoter + CpxR Forward 1924 BBa_K1486005 Arabinose promoter + sfGFP-CpxR Forward 2668 [Cterm] BBa_K1486009 CxpR & Split IFP1.4 [Nterm + Nterm] Forward 3726 BBa_K780000 Terminator for Bacillus subtilis 54 BBa_K864501 T22, P22 late terminator Forward 42 BBa_K864600 T0 (21 imm) transcriptional terminator Forward 52 BBa_K864601 Lambda t1 transcriptional terminator Forward BBa_B0011 LuxICDABEG (+/−) Bidirectional 46 BBa_B0014 double terminator (B0012-B0011) Bidirectional 95 BBa_B0021 LuxICDABEG (+/−), reversed Bidirectional 46 BBa_B0024 double terminator (B0012-B0011), Bidirectional 95 reversed BBa_B0050 Terminator (pBR322, +/−) Bidirectional 33 BBa_B0051 Terminator (yciA/tonA, +/−) Bidirectional 35 BBa_B1001 Terminator (artifical, small, % T~= 90) Bidirectional 34 BBa_B1007 Terminator (artificial, large, % T~= 80) Bidirectional 40 BBa_B1008 Terminator (artificial, large, % T~= 70) Bidirectional 40 BBa_B1009 Terminator (artificial, Bidirectional 40 large, % T~= 40%) BBa_K187025 terminator in pAB, BioBytes plasmid 60 BBa_K259006 GFP-Terminator Bidirectional 823 BBa_B0020 Terminator (Reverse B0010) Reverse 82 BBa_B0022 TE from coliphageT7, reversed Reverse 41 BBa_B0023 TE from coliphage T7, reversed Reverse 47 BBa_B0025 double terminator (B0015), reversed Reverse 129 BBa_B0052 Terminator (rrnC) Forward 41 BBa_B0060 Terminator (Reverse B0050) Bidirectional 33 BBa_B0061 Terminator (Reverse B0051) Bidirectional 35 BBa_B0063 Terminator (Reverse B0053) Reverse 72 Yeast and other Eukaryotes BBa_J63002 ADH1 terminator from S. cerevisiae Forward 225 BBa_K110012 STE2 terminator Forward 123 BBa_K1462070 cyc1 250 BBa_K1486025 ADH1 Terminator Forward 188 BBa_K392003 yeast ADH1 terminator 129 BBa_K801011 TEF1 yeast terminator 507 BBa_K801012 ADH1 yeast terminator 349 BBa_Y1015 CycE1 252 BBa_J52016 eukaryotic - derived from SV40 early Forward 238 poly A signal sequence BBa_J63002 ADH1 terminator from S. cerevisiae Forward 225 BBa_K110012 STE2 terminator Forward 123 BBa_K1159307 35S Terminator of Cauliflower Mosaic 217 Virus (CaMV) BBa_K1462070 cyc1 250 BBa_K1484215 nopaline synthase terminator 293 BBa_K1486025 ADH1 Terminator Forward 188 BBa_K392003 yeast ADH1 terminator 129 BBa_K404108 hGH terminator 481 BBa_K404116 hGH_[AAV2]-right-ITR 632 BBa_K678012 SV40 poly A, terminator for 139 mammalian cells BBa_K678018 hGH poly A, terminator for 635 mammalian cells BBa_K678019 BGH poly A, mammalian terminator 233 BBa_K678036 trpC terminator for Aspergillus 759 nidulans BBa_K678037 T1-motni, terminator for Aspergillus 1006 niger BBa_K678038 T2-motni, terminator for Aspergillus 990 niger BBa_K678039 T3-motni, terminator for Aspergillus 889 niger BBa_K801011 TEF1 yeast terminator 507 BBa_K801012 ADH1 yeast terminator 349 BBa_Y1015 CycE1 252 Corynebacterium Terminator Terminator Transcript Terminator Start End strand End DNA Sequence cg0001 1628 1647 + loop SEQ ID NO: 9 T1 cg0007 7504 7529 + stem 1 SEQ ID NO: 10 T2 cg0371 322229 322252 + stem 1 SEQ ID NO: 11 T3 cg0480 421697 421720 − stem 1 SEQ ID NO: 12 T4 cg0494 436587 436608 + loop SEQ ID NO: 13 T5 cg0564 499895 499917 + stem 1 SEQ ID NO: 14 T6 cg0610 541016 541039 + stem 2 SEQ ID NO: 15 T7 cg0695 613847 613868 − loop SEQ ID NO: 16 T8

Hypothesis-Driven Diversity Pools and Hill Climbing

The present disclosure teaches that the HTP genomic engineering methods of the present disclosure do not require prior genetic knowledge in order to achieve significant gains in host cell performance. Indeed, the present disclosure teaches methods of generating diversity pools via several functionally agnostic approaches, including random mutagenesis, and identification of genetic diversity among pre-existing host cell variants (e.g., such as the comparison between a wild type host cell and an industrial variant).

In some embodiments however, the present disclosure also teaches hypothesis-driven methods of designing genetic diversity mutations that will be used for downstream HTP engineering. That is, in some embodiments, the present disclosure teaches the directed design of selected mutations. In some embodiments, the directed mutations are incorporated into the engineering libraries of the present disclosure (e.g., SNP swap, PRO swap, or STOP swap).

In some embodiments, the present disclosure teaches the creation of directed mutations based on gene annotation, hypothesized (or confirmed) gene function, or location within a genome. The diversity pools of the present disclosure may include mutations in genes hypothesized to be involved in a specific metabolic or genetic pathway associated in the literature with increased performance of a host cell. In other embodiments, the diversity pool of the present disclosure may also include mutations to genes present in an operon associated with improved host performance. In yet other embodiments, the diversity pool of the present disclosure may also include mutations to genes based on algorithmic predicted function, or other gene annotation.

In some embodiments, the present disclosure teaches a “shell” based approach for prioritizing the targets of hypothesis-driven mutations. The shell metaphor for target prioritization is based on the hypothesis that only a handful of primary genes are responsible for most of a particular aspect of a host cell's performance (e.g., production of a single biomolecule). These primary genes are located at the core of the shell, followed by secondary effect genes in the second layer, tertiary effects in the third shell, and . . . etc. For example, in one embodiment the core of the shell might comprise genes encoding critical biosynthetic enzymes within a selected metabolic pathway (e.g., production of citric acid). Genes located on the second shell might comprise genes encoding for other enzymes within the biosynthetic pathway responsible for product diversion or feedback signaling. Third tier genes under this illustrative metaphor would likely comprise regulatory genes responsible for modulating expression of the biosynthetic pathway, or for regulating general carbon flux within the host cell.

The present disclosure also teaches “hill climb” methods for optimizing performance gains from every identified mutation. In some embodiments, the present disclosure teaches that random, natural, or hypothesis-driven mutations in HTP diversity libraries can result in the identification of genes associated with host cell performance. For example, the present methods may identify one or more beneficial SNPs located on, or near, a gene coding sequence. This gene might be associated with host cell performance, and its identification can be analogized to the discovery of a performance “hill” in the combinatorial genetic mutation space of an organism.

In some embodiments, the present disclosure teaches methods of exploring the combinatorial space around the identified hill embodied in the SNP mutation. That is, in some embodiments, the present disclosure teaches the perturbation of the identified gene and associated regulatory sequences in order to optimize performance gains obtained from that gene node (i.e., hill climbing). Thus, according to the methods of the present disclosure, a gene might first be identified in a diversity library sourced from random mutagenesis, but might be later improved for use in the strain improvement program through the directed mutation of another sequence within the same gene.

The concept of hill climbing can also be expanded beyond the exploration of the combinatorial space surrounding a single gene sequence. In some embodiments, a mutation in a specific gene might reveal the importance of a particular metabolic or genetic pathway to host cell performance. For example, in some embodiments, the discovery that a mutation in a single RNA degradation gene resulted in significant host performance gains could be used as a basis for mutating related RNA degradation genes as a means for extracting additional performance gains from the host organism. Persons having skill in the art will recognize variants of the above describe shell and hill climb approaches to directed genetic design. High-throughput Screening.

Cell Culture and Fermentation

Cells of the present disclosure can be cultured in conventional nutrient media modified as appropriate for any desired biosynthetic reactions or selections. In some embodiments, the present disclosure teaches culture in inducing media for activating promoters. In some embodiments, the present disclosure teaches media with selection agents, including selection agents of transformants (e.g., antibiotics), or selection of organisms suited to grow under inhibiting conditions (e.g., high ethanol conditions). In some embodiments, the present disclosure teaches growing cell cultures in media optimized for cell growth. In other embodiments, the present disclosure teaches growing cell cultures in media optimized for product yield. In some embodiments, the present disclosure teaches growing cultures in media capable of inducing cell growth and also contains the necessary precursors for final product production (e.g., high levels of sugars for ethanol production).

Culture conditions, such as temperature, pH and the like, are those suitable for use with the host cell selected for expression, and will be apparent to those skilled in the art. As noted, many references are available for the culture and production of many cells, including cells of bacterial, plant, animal (including mammalian) and archaebacterial origin. See e.g., Sambrook, Ausubel (all supra), as well as Berger, Guide to Molecular Cloning Techniques, Methods in Enzymology volume 152 Academic Press, Inc., San Diego, Calif.; and Freshney (1994) Culture of Animal Cells, a Manual of Basic Technique, third edition, Wiley-Liss, New York and the references cited therein; Doyle and Griffiths (1997)Mammalian Cell Culture: Essential Techniques John Wiley and Sons, NY; Humason (1979) Animal Tissue Techniques, fourth edition W.H. Freeman and Company; and Ricciardelle et al., (1989) In Vitro Cell Dev. Biol. 25:1016-1024, all of which are incorporated herein by reference. For plant cell culture and regeneration, Payne et al. (1992) Plant Cell and Tissue Culture in Liquid Systems John Wiley & Sons, Inc. New York, N.Y.; Gamborg and Phillips (eds) (1995) Plant Cell, Tissue and Organ Culture; Fundamental Methods Springer Lab Manual, Springer-Verlag (Berlin Heidelberg N.Y.); Jones, ed. (1984) Plant Gene Transfer and Expression Protocols, Humana Press, Totowa, N.J. and Plant Molecular Biology (1993) R. R. D. Croy, Ed. Bios Scientific Publishers, Oxford, U.K. ISBN 0 12 198370 6, all of which are incorporated herein by reference. Cell culture media in general are set forth in Atlas and Parks (eds.) The Handbook of Microbiological Media (1993) CRC Press, Boca Raton, Fla., which is incorporated herein by reference. Additional information for cell culture is found in available commercial literature such as the Life Science Research Cell Culture Catalogue from Sigma-Aldrich, Inc (St Louis, Mo.) (“Sigma-LSRCCC”) and, for example, The Plant Culture Catalogue and supplement also from Sigma-Aldrich, Inc (St Louis, Mo.) (“Sigma-PCCS”), all of which are incorporated herein by reference.

The culture medium to be used must in a suitable manner satisfy the demands of the respective strains. Descriptions of culture media for various microorganisms are present in the “Manual of Methods for General Bacteriology” of the American Society for Bacteriology (Washington D.C., USA, 1981).

The present disclosure furthermore provides a process for fermentative preparation of a product of interest, comprising the steps of: a) culturing a microorganism according to the present disclosure in a suitable medium, resulting in a fermentation broth; and b) concentrating the product of interest in the fermentation broth of a) and/or in the cells of the microorganism.

In some embodiments, the present disclosure teaches that the microorganisms produced may be cultured continuously—as described, for example, in WO 05/021772—or discontinuously in a batch process (batch cultivation) or in a fed-batch or repeated fed-batch process for the purpose of producing the desired organic-chemical compound. A summary of a general nature about known cultivation methods is available in the textbook by Chmiel (Bioprozeßechnik. 1: Einführung in die Bioverfahrenstechnik (Gustav Fischer Verlag, Stuttgart, 1991)) or in the textbook by Storhas (Bioreaktoren and periphere Einrichtungen (Vieweg Verlag, Braunschweig/Wiesbaden, 1994)).

In some embodiments, the cells of the present disclosure are grown under batch or continuous fermentations conditions.

Classical batch fermentation is a closed system, wherein the compositions of the medium is set at the beginning of the fermentation and is not subject to artificial alternations during the fermentation. A variation of the batch system is a fed-batch fermentation which also finds use in the present disclosure. In this variation, the substrate is added in increments as the fermentation progresses. Fed-batch systems are useful when catabolite repression is likely to inhibit the metabolism of the cells and where it is desirable to have limited amounts of substrate in the medium. Batch and fed-batch fermentations are common and well known in the art.

Continuous fermentation is a system where a defined fermentation medium is added continuously to a bioreactor and an equal amount of conditioned medium is removed simultaneously for processing and harvesting of desired biomolecule products of interest. In some embodiments, continuous fermentation generally maintains the cultures at a constant high density where cells are primarily in log phase growth. In some embodiments, continuous fermentation generally maintains the cultures at a stationary or late log/stationary, phase growth. Continuous fermentation systems strive to maintain steady state growth conditions.

Methods for modulating nutrients and growth factors for continuous fermentation processes as well as techniques for maximizing the rate of product formation are well known in the art of industrial microbiology.

For example, a non-limiting list of carbon sources for the cultures of the present disclosure include, sugars and carbohydrates such as, for example, glucose, sucrose, lactose, fructose, maltose, molasses, sucrose-containing solutions from sugar beet or sugar cane processing, starch, starch hydrolysate, and cellulose; oils and fats such as, for example, soybean oil, sunflower oil, groundnut oil and coconut fat; fatty acids such as, for example, palmitic acid, stearic acid, and linoleic acid; alcohols such as, for example, glycerol, methanol, and ethanol; and organic acids such as, for example, acetic acid or lactic acid.

A non-limiting list of the nitrogen sources for the cultures of the present disclosure include, organic nitrogen-containing compounds such as peptones, yeast extract, meat extract, malt extract, corn steep liquor, soybean flour, and urea; or inorganic compounds such as ammonium sulfate, ammonium chloride, ammonium phosphate, ammonium carbonate, and ammonium nitrate. The nitrogen sources can be used individually or as a mixture.

A non-limiting list of the possible phosphorus sources for the cultures of the present disclosure include, phosphoric acid, potassium dihydrogen phosphate or dipotassium hydrogen phosphate or the corresponding sodium-containing salts.

The culture medium may additionally comprise salts, for example in the form of chlorides or sulfates of metals such as, for example, sodium, potassium, magnesium, calcium and iron, such as, for example, magnesium sulfate or iron sulfate, which are necessary for growth.

Finally, essential growth factors such as amino acids, for example homoserine and vitamins, for example thiamine, biotin or pantothenic acid, may be employed in addition to the abovementioned substances.

In some embodiments, the pH of the culture can be controlled by any acid or base, or buffer salt, including, but not limited to sodium hydroxide, potassium hydroxide, ammonia, or aqueous ammonia; or acidic compounds such as phosphoric acid or sulfuric acid in a suitable manner. In some embodiments, the pH is generally adjusted to a value of from 6.0 to 8.5, preferably 6.5 to 8.

In some embodiments, the cultures of the present disclosure may include an anti-foaming agent such as, for example, fatty acid polyglycol esters. In some embodiments the cultures of the present disclosure are modified to stabilize the plasmids of the cultures by adding suitable selective substances such as, for example, antibiotics.

In some embodiments, the culture is carried out under aerobic conditions. In order to maintain these conditions, oxygen or oxygen-containing gas mixtures such as, for example, air are introduced into the culture. It is likewise possible to use liquids enriched with hydrogen peroxide. The fermentation is carried out, where appropriate, at elevated pressure, for example at an elevated pressure of from 0.03 to 0.2 MPa. The temperature of the culture is normally from 20° C. to 45° C. and preferably from 25° C. to 40° C., particularly preferably from 30° C. to 37° C. In batch or fed-batch processes, the cultivation is preferably continued until an amount of the desired product of interest (e.g. an organic-chemical compound) sufficient for being recovered has formed. This aim can normally be achieved within 10 hours to 160 hours. In continuous processes, longer cultivation times are possible. The activity of the microorganisms results in a concentration (accumulation) of the product of interest in the fermentation medium and/or in the cells of said microorganisms.

In some embodiments, the culture is carried out under anaerobic conditions.

Screening

In some embodiments, the present disclosure teaches high-throughput initial screenings. In other embodiments, the present disclosure also teaches robust tank-based validations of performance data (see FIG. 6B).

In some embodiments, the high-throughput screening process is designed to predict performance of strains in bioreactors. As previously described, culture conditions are selected to be suitable for the organism and reflective of bioreactor conditions. Individual colonies are picked and transferred into 96 well plates and incubated for a suitable amount of time. Cells are subsequently transferred to new 96 well plates for additional seed cultures, or to production cultures. Cultures are incubated for varying lengths of time, where multiple measurements may be made. These may include measurements of product, biomass or other characteristics that predict performance of strains in bioreactors. High-throughput culture results are used to predict bioreactor performance.

In some embodiments, the tank-based performance validation is used to confirm performance of strains isolated by high throughput screening. Fermentation processes/conditions are obtained from client sites. Candidate strains are screened using bench scale fermentation reactors (e.g., reactors disclosed in Table 5 of the present disclosure) for relevant strain performance characteristics such as productivity or yield.

Product Recovery and Quantification

Methods for screening for the production of products of interest are known to those of skill in the art and are discussed throughout the present specification. Such methods may be employed when screening the strains of the disclosure.

In some embodiments, the present disclosure teaches methods of improving strains designed to produce non-secreted intracellular products. For example, the present disclosure teaches methods of improving the robustness, yield, efficiency, or overall desirability of cell cultures producing intracellular enzymes, oils, pharmaceuticals, or other valuable small molecules or peptides. The recovery or isolation of non-secreted intracellular products can be achieved by lysis and recovery techniques that are well known in the art, including those described herein.

For example, in some embodiments, cells of the present disclosure can be harvested by centrifugation, filtration, settling, or other method. Harvested cells are then disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing agents, or other methods, which are well known to those skilled in the art.

The resulting product of interest, e.g. a polypeptide, may be recovered/isolated and optionally purified by any of a number of methods known in the art. For example, a product polypeptide may be isolated from the nutrient medium by conventional procedures including, but not limited to: centrifugation, filtration, extraction, spray-drying, evaporation, chromatography (e.g., ion exchange, affinity, hydrophobic interaction, chromatofocusing, and size exclusion), or precipitation. Finally, high performance liquid chromatography (HPLC) can be employed in the final purification steps. (See for example Purification of intracellular protein as described in Parry et al., 2001, Biochem. 1353:117, and Hong et al., 2007, Appl. Microbiol. Biotechnol. 73:1331, both incorporated herein by reference).

In addition to the references noted supra, a variety of purification methods are well known in the art, including, for example, those set forth in: Sandana (1997) Bioseparation of Proteins, Academic Press, Inc.; Bollag et al. (1996) Protein Methods, 2^(nd) Edition, Wiley-Liss, N.Y.; Walker (1996) The Protein Protocols Handbook Humana Press, NJ; Harris and Angal (1990) Protein Purification Applications: A Practical Approach, IRL Press at Oxford, Oxford, England; Harris and Angal Protein Purification Methods: A Practical Approach, IRL Press at Oxford, Oxford, England; Scopes (1993) Protein Purification: Principles and Practice 3^(rd) Edition, Springer Verlag, N.Y.; Janson and Ryden (1998) Protein Purification: Principles, High Resolution Methods and Applications, Second Edition, Wiley-VCH, NY; and Walker (1998) Protein Protocols on CD-ROM, Humana Press, NJ, all of which are incorporated herein by reference.

In some embodiments, the present disclosure teaches the methods of improving strains designed to produce secreted products. For example, the present disclosure teaches methods of improving the robustness, yield, efficiency, or overall desirability of cell cultures producing valuable small molecules or peptides.

In some embodiments, immunological methods may be used to detect and/or purify secreted or non-secreted products produced by the cells of the present disclosure. In one example approach, antibody raised against a product molecule (e.g., against an insulin polypeptide or an immunogenic fragment thereof) using conventional methods is immobilized on beads, mixed with cell culture media under conditions in which the endoglucanase is bound, and precipitated. In some embodiments, the present disclosure teaches the use of enzyme-linked immunosorbent assays (ELISA).

In other related embodiments, immunochromatography is used, as disclosed in U.S. Pat. Nos. 5,591,645, 4,855,240, 4,435,504, 4,980,298, and Se-Hwan Paek, et al., “Development of rapid One-Step Immunochromatographic assay, Methods”, 22, 53-60, 2000), each of which are incorporated by reference herein. A general immunochromatography detects a specimen by using two antibodies. A first antibody exists in a test solution or at a portion at an end of a test piece in an approximately rectangular shape made from a porous membrane, where the test solution is dropped. This antibody is labeled with latex particles or gold colloidal particles (this antibody will be called as a labeled antibody hereinafter). When the dropped test solution includes a specimen to be detected, the labeled antibody recognizes the specimen so as to be bonded with the specimen. A complex of the specimen and labeled antibody flows by capillarity toward an absorber, which is made from a filter paper and attached to an end opposite to the end having included the labeled antibody. During the flow, the complex of the specimen and labeled antibody is recognized and caught by a second antibody (it will be called as a tapping antibody hereinafter) existing at the middle of the porous membrane and, as a result of this, the complex appears at a detection part on the porous membrane as a visible signal and is detected.

In some embodiments, the screening methods of the present disclosure are based on photometric detection techniques (absorption, fluorescence). For example, in some embodiments, detection may be based on the presence of a fluorophore detector such as GFP bound to an antibody. In other embodiments, the photometric detection may be based on the accumulation on the desired product from the cell culture. In some embodiments, the product may be detectable via UV of the culture or extracts from said culture.

Persons having skill in the art will recognize that the methods of the present disclosure are compatible with host cells producing any desirable biomolecule product of interest. Table 2 below presents a non-limiting list of the product categories, biomolecules, and host cells, included within the scope of the present disclosure. These examples are provided for illustrative purposes, and are not meant to limit the applicability of the presently disclosed technology in any way.

TABLE 2 A non-limiting list of the host cells and products of interest of the present disclosure. Product category Products Host category Hosts Amino acids Lysine Bacteria Corynebacterium glutamicum Amino acids Methionine Bacteria Escherichia coli Amino acids MSG Bacteria Corynebacterium glutamicum Amino acids Threonine Bacteria Escherichia coli Amino acids Threonine Bacteria Corynebacterium glutamicum Amino acids Tryptophan Bacteria Corynebacterium glutamicum Enzymes Enzymes (11) Filamentous fungi Trichoderma reesei Enzymes Enzymes (11) Fungi Myceliopthora thermophila (C1) Enzymes Enzymes (11) Filamentous fungi Aspergillus oryzae Enzymes Enzymes (11) Filamentous fungi Aspergillus niger Enzymes Enzymes (11) Bacteria Bacillus subtilis Enzymes Enzymes (11) Bacteria Bacillus licheniformis Enzymes Enzymes (11) Bacteria Bacillus clausii Flavor & Agarwood Yeast Saccharomyces cerevisiae Fragrance Flavor & Ambrox Yeast Saccharomyces cerevisiae Fragrance Flavor & Nootkatone Yeast Saccharomyces cerevisiae Fragrance Flavor & Patchouli oil Yeast Saccharomyces cerevisiae Fragrance Flavor & Saffron Yeast Saccharomyces cerevisiae Fragrance Flavor & Sandalwood oil Yeast Saccharomyces cerevisiae Fragrance Flavor & Valencene Yeast Saccharomyces cerevisiae Fragrance Flavor & Vanillin Yeast Saccharomyces cerevisiae Fragrance Food CoQ10/Ubiquinol Yeast Schizosaccharomyces pombe Food Omega 3 fatty Microalgae Schizochytrium acids Food Omega 6 fatty Microalgae Schizochytrium acids Food Vitamin B12 Bacteria Propionibacterium freudenreichii Food Vitamin B2 Filamentous fungi Ashbya gossypii Food Vitamin B2 Bacteria Bacillus subtilis Food Erythritol Yeast-like fungi Torula coralline Food Erythritol Yeast-like fungi Pseudozyma tsukubaensis Food Erythritol Yeast-like fungi Moniliella pollinis Food Steviol Yeast Saccharomyces cerevisiae glycosides Hydrocolloids Diutan gum Bacteria Sphingomonas sp Hydrocolloids Gellan gum Bacteria Sphingomonas elodea Hydrocolloids Xanthan gum Bacteria Xanthomonas campestris Intermediates 1,3-PDO Bacteria Escherichia coli Intermediates 1,4-BDO Bacteria Escherichia coli Intermediates Butadiene Bacteria Cupriavidus necator Intermediates n-butanol Bacteria (obligate Clostridium acetobutylicum anaerobe) Organic acids Citric acid Filamentous fungi Aspergillus niger Organic acids Citric acid Yeast Pichia guilliermondii Organic acids Gluconic acid Filamentous fungi Aspergillus niger Organic acids Itaconic acid Filamentous fungi Aspergillus terreus Organic acids Lactic acid Bacteria Lactobacillus Organic acids Lactic acid Bacteria Geobacillus thermoglucosidasius Organic acids LCDAs-DDDA Yeast Candida Polyketides/Ag Spinosad Yeast Saccharopolyspora spinosa Polyketides/Ag Spinetoram Yeast Saccharopolyspora spinosa

Selection Criteria and Goals

The selection criteria applied to the methods of the present disclosure will vary with the specific goals of the strain improvement program. The present disclosure may be adapted to meet any program goals. For example, in some embodiments, the program goal may be to maximize single batch yields of reactions with no immediate time limits. In other embodiments, the program goal may be to rebalance biosynthetic yields to produce a specific product, or to produce a particular ratio of products. In other embodiments, the program goal may be to modify the chemical structure of a product, such as lengthening the carbon chain of a polymer. In some embodiments, the program goal may be to improve performance characteristics such as yield, titer, productivity, by-product elimination, tolerance to process excursions, optimal growth temperature and growth rate. In some embodiments, the program goal is improved host performance as measured by volumetric productivity, specific productivity, yield or titre, of a product of interest produced by a microbe.

In other embodiments, the program goal may be to optimize synthesis efficiency of a commercial strain in terms of final product yield per quantity of inputs (e.g., total amount of ethanol produced per pound of sucrose). In other embodiments, the program goal may be to optimize synthesis speed, as measured for example in terms of batch completion rates, or yield rates in continuous culturing systems. In other embodiments, the program goal may be to increase strain resistance to a particular phage, or otherwise increase strain vigor/robustness under culture conditions.

In some embodiments, strain improvement projects may be subject to more than one goal. In some embodiments, the goal of the strain project may hinge on quality, reliability, or overall profitability. In some embodiments, the present disclosure teaches methods of associated selected mutations or groups of mutations with one or more of the strain properties described above.

Persons having ordinary skill in the art will recognize how to tailor strain selection criteria to meet the particular project goal. For example, selections of a strain's single batch max yield at reaction saturation may be appropriate for identifying strains with high single batch yields. Selection based on consistency in yield across a range of temperatures and conditions may be appropriate for identifying strains with increased robustness and reliability.

In some embodiments, the selection criteria for the initial high-throughput phase and the tank-based validation will be identical. In other embodiments, tank-based selection may operate under additional and/or different selection criteria. For example, in some embodiments, high-throughput strain selection might be based on single batch reaction completion yields, while tank-based selection may be expanded to include selections based on yields for reaction speed.

Sequencing

In some embodiments, the present disclosure teaches whole-genome sequencing of the organisms described herein. In other embodiments, the present disclosure also teaches sequencing of plasmids, PCR products, and other oligos as quality controls to the methods of the present disclosure. Sequencing methods for large and small projects are well known to those in the art.

In some embodiments, any high-throughput technique for sequencing nucleic acids can be used in the methods of the disclosure. In some embodiments, the present disclosure teaches whole genome sequencing. In other embodiments, the present disclosure teaches amplicon sequencing ultra deep sequencing to identify genetic variations. In some embodiments, the present disclosure also teaches novel methods for library preparation, including tagmentation (see WO/2016/073690). DNA sequencing techniques include classic dideoxy sequencing reactions (Sanger method) using labeled terminators or primers and gel separation in slab or capillary; sequencing by synthesis using reversibly terminated labeled nucleotides, pyrosequencing; 454 sequencing; allele specific hybridization to a library of labeled oligonucleotide probes; sequencing by synthesis using allele specific hybridization to a library of labeled clones that is followed by ligation; real time monitoring of the incorporation of labeled nucleotides during a polymerization step; polony sequencing; and SOLiD sequencing.

In one aspect of the disclosure, high-throughput methods of sequencing are employed that comprise a step of spatially isolating individual molecules on a solid surface where they are sequenced in parallel. Such solid surfaces may include nonporous surfaces (such as in Solexa sequencing, e.g. Bentley et al, Nature, 456: 53-59 (2008) or Complete Genomics sequencing, e.g. Drmanac et al, Science, 327: 78-81 (2010)), arrays of wells, which may include bead- or particle-bound templates (such as with 454, e.g. Margulies et al, Nature, 437: 376-380 (2005) or Ion Torrent sequencing, U.S. patent publication 2010/0137143 or 2010/0304982), micromachined membranes (such as with SMRT sequencing, e.g. Eid et al, Science, 323: 133-138 (2009)), or bead arrays (as with SOLiD sequencing or polony sequencing, e.g. Kim et al, Science, 316: 1481-1414 (2007)).

In another embodiment, the methods of the present disclosure comprise amplifying the isolated molecules either before or after they are spatially isolated on a solid surface. Prior amplification may comprise emulsion-based amplification, such as emulsion PCR, or rolling circle amplification. Also taught is Solexa-based sequencing where individual template molecules are spatially isolated on a solid surface, after which they are amplified in parallel by bridge PCR to form separate clonal populations, or clusters, and then sequenced, as described in Bentley et al (cited above) and in manufacturer's instructions (e.g. TruSeq™ Sample Preparation Kit and Data Sheet, Illumina, Inc., San Diego, Calif., 2010); and further in the following references: U.S. Pat. Nos. 6,090,592; 6,300,070; 7,115,400; and EP0972081B1; which are incorporated by reference.

In one embodiment, individual molecules disposed and amplified on a solid surface form clusters in a density of at least 10⁵ clusters per my; or in a density of at least 5×10⁵ per my; or in a density of at least 10⁶ clusters per cm². In one embodiment, sequencing chemistries are employed having relatively high error rates. In such embodiments, the average quality scores produced by such chemistries are monotonically declining functions of sequence read lengths. In one embodiment, such decline corresponds to 0.5 percent of sequence reads have at least one error in positions 1-75; 1 percent of sequence reads have at least one error in positions 76-100; and 2 percent of sequence reads have at least one error in positions 101-125.

Computational Analysis and Prediction of Effects of Genome-Wide Genetic Design Criteria

In some embodiments, the present disclosure teaches methods of predicting the effects of particular genetic alterations being incorporated into a given host strain. In further aspects, the disclosure provides methods for generating proposed genetic alterations that should be incorporated into a given host strain, in order for said host to possess a particular phenotypic trait or strain parameter. In given aspects, the disclosure provides predictive models that can be utilized to design novel host strains.

In some embodiments, the present disclosure teaches methods of analyzing the performance results of each round of screening and methods for generating new proposed genome-wide sequence modifications predicted to enhance strain performance in the following round of screening.

In some embodiments, the present disclosure teaches that the system generates proposed sequence modifications to host strains based on previous screening results. In some embodiments, the recommendations of the present system are based on the results from the immediately preceding screening. In other embodiments, the recommendations of the present system are based on the cumulative results of one or more of the preceding screenings.

In some embodiments, the recommendations of the present system are based on previously developed HTP genetic design libraries. For example, in some embodiments, the present system is designed to save results from previous screenings, and apply those results to a different project, in the same or different host organisms.

In other embodiments, the recommendations of the present system are based on scientific insights. For example, in some embodiments, the recommendations are based on known properties of genes (from sources such as annotated gene databases and the relevant literature), codon optimization, transcriptional slippage, uORFs, or other hypothesis driven sequence and host optimizations.

In some embodiments, the proposed sequence modifications to a host strain recommended by the system, or predictive model, are carried out by the utilization of one or more of the disclosed molecular tools sets comprising: (1) Promoter swaps, (2) SNP swaps, (3) Start/Stop codon exchanges, (4) Sequence optimization, (5) Stop swaps, and (5) Epistasis mapping.

The HTP genetic engineering platform described herein is agnostic with respect to any particular microbe or phenotypic trait (e.g. production of a particular compound). That is, the platform and methods taught herein can be utilized with any host cell to engineer said host cell to have any desired phenotypic trait. Furthermore, the lessons learned from a given HTP genetic engineering process used to create one novel host cell, can be applied to any number of other host cells, as a result of the storage, characterization, and analysis of a myriad of process parameters that occurs during the taught methods.

As alluded to in the epistatic mapping section, it is possible to estimate the performance (a.k.a. score) of a hypothetical strain obtained by consolidating a collection of mutations from a HTP genetic design library into a particular background via some preferred predictive model. Given such a predictive model, it is possible to score and rank all hypothetical strains accessible to the mutation library via combinatorial consolidation. The below section outlines particular models utilized in the present HTP platform.

Predictive Strain Design

Described herein is an approach for predictive strain design, including: methods of describing genetic changes and strain performance, predicting strain performance based on the composition of changes in the strain, recommending candidate designs with high predicted performance, and filtering predictions to optimize for second-order considerations, e.g. similarity to existing strains, epistasis, or confidence in predictions.

Inputs to Strain Design Model

In one embodiment, for the sake of ease of illustration, input data may comprise two components: (1) sets of genetic changes and (2) relative strain performance. Those skilled in the art will recognize that this model can be readily extended to consider a wide variety of inputs, while keeping in mind the countervailing consideration of overfitting. In addition to genetic changes, some of the input parameters (independent variables) that can be adjusted are cell types (genus, species, strain, phylogenetic characterization, etc.) and process parameters (e.g., environmental conditions, handling equipment, modification techniques, etc.) under which fermentation is conducted with the cells.

The sets of genetic changes can come from the previously discussed collections of genetic perturbations termed HTP genetic design libraries. The relative strain performance can be assessed based upon any given parameter or phenotypic trait of interest (e.g. production of a compound, small molecule, or product of interest).

Cell types can be specified in general categories such as prokaryotic and eukaryotic systems, genus, species, strain, tissue cultures (vs. disperse cells), etc. Process parameters that can be adjusted include temperature, pressure, reactor configuration, and medium composition. Examples of reactor configuration include the volume of the reactor, whether the process is a batch or continuous, and, if continuous, the volumetric flow rate, etc. One can also specify the support structure, if any, on which the cells reside. Examples of medium composition include the concentrations of electrolytes, nutrients, waste products, acids, pH, and the like.

Sets of Genetic Changes from Selected HTP Genetic Design Libraries to be Utilized in the Initial Linear Regression Model that Subsequently is Used to Create the Predictive Strain Design Model

An example set of entries from a table of genetic changes is shown below in Table 3. Each row indicates a genetic change in strain 7000051473, as well as metadata about the mechanism of change, e.g. promoter swap or SNP swap. aceE, zwf, and pyc are all related to the citric acid cycle.

In this case strain 7000051473 has a total of 7 changes. “Last change” means the change in this strain represents the most recent modification in this strain lineage. Thus, comparing this strain's performance to the performance of its parent represents a data point concerning the performance of the “last change” mutation.

TABLE 3 Strain design entry table for strain 7000051473 strain name library change from to last_change 7000051473 dlc19_42 proswp pcg3121 cg1144 pcg3121_cg1144 1 7000051473 dlc19_42 scswp acee atg > ttg ttg acee_atg 0 7000051473 dlc19_42 snpswp dss_033 NA na 0 7000051473 dlc19_42 snpswp dss_084 NA t 0 7000051473 dlc19_42 snpswp dss_316 NA na 0 7000051473 dlc19_42 proswp pcg0007_39 zwf pcg0007_39_zwf 0 7000051473 dlc19_42 proswp pcg1860 pyc pcg1860_pyc 0

Built Strain Performance Assessment

The goal of the taught model is to predict strain performance based on the composition of genetic changes introduced to the strain. To construct a standard for comparison, strain performance is computed relative to a common reference strain, by first calculating the median performance per strain, per assay plate. Relative performance is then computed as the difference in average performance between an engineered strain and the common reference strain within the same plate. Restricting the calculations to within-plate comparisons ensures that the samples under consideration all received the same experimental conditions.

FIG. 23 shows the distribution of relative strain performances for the input data under consideration. A relative performance of zero indicates that the engineered strain performed equally well to the in-plate base or “reference” strain. Of interest is the ability of the predictive model to identify the strains that are likely to perform significantly above zero. Further, and more generally, of interest is whether any given strain outperforms its parent by some criteria. In practice, the criteria can be a product titer meeting or exceeding some threshold above the parent level, though having a statistically significant difference from the parent in the desired direction could also be used instead or in addition. The role of the base or “reference” strain is simply to serve as an added normalization factor for making comparisons within or between plates.

A concept to keep in mind is that of differences between: parent strain and reference strain. The parent strain is the background that was used for a current round of mutagenesis. The reference strain is a control strain run in every plate to facilitate comparisons, especially between plates, and is typically the “base strain” as referenced above. But since the base strain (e.g., the wild-type or industrial strain being used to benchmark overall performance) is not necessarily a “base” in the sense of being a mutagenesis target in a given round of strain improvement, a more descriptive term is “reference strain.”

In summary, a base/reference strain is used to benchmark the performance of built strains, generally, while the parent strain is used to benchmark the performance of a specific genetic change in the relevant genetic background.

Ranking the Performance of Built Strains with Linear Regression

The goal of the disclosed model is to rank the performance of built strains, by describing relative strain performance, as a function of the composition of genetic changes introduced into the built strains. As discussed throughout the disclosure, the various HTP genetic design libraries provide the repertoire of possible genetic changes (e.g., genetic perturbations/alterations) that are introduced into the engineered strains. Linear regression is the basis for the currently described exemplary predictive model.

The below table contains example input for regression-based modeling. The strain performances are ranked relative to a common base strain, as a function of the composition of the genetic changes contained in the strain.

Each column heading represents a genetic change, a “1” represents the presence of the change, whereas a “0” represents the absence of a change. “DSS” refers to SNP swaps from a particular library (first 3 columns after relative perf). The last 3 columns are promoter swaps, where the pcgXXXX denotes the particular promoter, and the last 3 letters represent the gene the promoter is being applied to. The genes are related to central metabolism. The promoters are from Corynebacterium glutamicum (hence the “cg” notation). Further information on the utilized promoters can be found in Table 1, listing promoters P1-P8, and the sequence listing of the present application. Further, detailed information on each promoter P1-P8 can be found in U.S. Provisional Application No. 62/264,232, filed on Dec. 7, 2015, and entitled “Promoters from Corynebacterium glutamicum,” which is incorporated herein by reference. For ease of reference, in the below table, pcg3121=P8; pcg0755=P4; and pcg1860=P3.

TABLE 4 Summary of genetic changes and their effect on relative performance. relative_perf dss_033 dss_034 dss_056 pcg3121_pgi pcg0755_zwf pcg1860_pyc 0.1358908 0 0 0 0 0 1 −1.8946985 1 0 0 1 0 1 −0.0222045 0 0 0 1 0 0 0.6342183 1 0 1 0 0 0 −0.0803285 1 1 0 0 0 0 2.6468117 0 0 0 1 0 0 Linear Regression to Characterize Built Strains

Linear regression is an attractive method for the described HTP genomic engineering platform, because of the ease of implementation and interpretation. The resulting regression coefficients can be interpreted as the average increase or decrease in relative strain performance attributable to the presence of each genetic change.

For example, as seen in FIG. 24, this technique allows us to conclude that changing the pgi promoter to pcg3121 improves relative strain performance by approximately 5 units on average and is thus a potentially highly desirable change, in the absence of any negative epistatic interactions (note: the input is a unit-less normalized value).

The taught method therefore uses linear regression models to describe/characterize and rank built strains, which have various genetic perturbations introduced into their genomes from the various taught libraries.

Predictive Design Modeling

The linear regression model described above, which utilized data from constructed strains, can be used to make performance predictions for strains that haven't yet been built.

The procedure can be summarized as follows: generate in silico all possible configurations of genetic changes→use the regression model to predict relative strain performance→order the candidate strain designs by performance. Thus, by utilizing the regression model to predict the performance of as-yet-unbuilt strains, the method allows for the production of higher performing strains, while simultaneously conducting fewer experiments.

Generate Configurations

When constructing a model to predict performance of as-yet-unbuilt strains, the first step is to produce a sequence of design candidates. This is done by fixing the total number of genetic changes in the strain, and then defining all possible combinations of genetic changes. For example, one can set the total number of potential genetic changes/perturbations to 29 (e.g. 29 possible SNPs, or 29 different promoters, or any combination thereof as long as the universe of genetic perturbations is 29) and then decide to design all possible 3-member combinations of the 29 potential genetic changes, which will result in 3,654 candidate strain designs.

To provide context to the aforementioned 3,654 candidate strains, consider that one can calculate the number of non-redundant groupings of size r from n possible members using n!/((n−r)!*r!). If r=3, n=29 gives 3,654. Thus, if one designs all possible 3-member combinations of 29 potential changes the results is 3,654 candidate strains. The 29 potential genetic changes are present in the x-axis of FIG. 25.

Predict Performance of New Strain Designs

Using the linear regression constructed above with the combinatorial configurations as input, one can then predict the expected relative performance of each candidate design. FIG. 25 summarizes the composition of changes for the top 100 predicted strain designs. The x-axis lists the pool of potential genetic changes (29 possible genetic changes), and the y-axis shows the rank order. Black cells indicate the presence of a particular change in the candidate design, while white cells indicate the absence of that change. In this particular example, all of the top 100 designs contain the changes pcg3121_pgi, pcg1860_pyc, dss_339, and pcg0007_39_lysa. Additionally, the top candidate design contains the changes dss_034, dss_009.

Predictive accuracy should increase over time as new observations are used to iteratively retrain and refit the model. Results from a study by the inventors illustrate the methods by which the predictive model can be iteratively retrained and improved. FIG. 47 compares model predictions with observed measurement values. The quality of model predictions can be assessed through several methods, including a correlation coefficient indicating the strength of association between the predicted and observed values, or the root-mean-square error, which is a measure of the average model error. Using a chosen metric for model evaluation, the system may define rules for when the model should be retrained.

A couple of unstated assumptions to the above model include: (1) there are no epistatic interactions; and (2) the genetic changes/perturbations utilized to build the predictive model (e.g. from built strain data as illustrated in FIG. 24, or whatever data set is used as the reference to construct the model) were all made in the same background, as the proposed combinations of genetic changes (e.g. as illustrated in FIG. 25).

Filtering for Second-Order Features

The above illustrative example focused on linear regression predictions based on predicted host cell performance. In some embodiments, the present linear regression methods can also be applied to non-biomolecule factors, such as saturation biomass, resistance, or other measurable host cell features. Thus the methods of the present disclosure also teach in considering other features outside of predicted performance when prioritizing the candidates to build. Assuming there is additional relevant data, nonlinear terms are also included in the regression model.

Closeness with Existing Strains

Predicted strains that are similar to ones that have already been built could result in time and cost savings despite not being a top predicted candidate

Diversity of Changes

When constructing the aforementioned models, one cannot be certain that genetic changes will truly be additive (as assumed by linear regression and mentioned as an assumption above) due to the presence of epistatic interactions. Therefore, knowledge of genetic change dissimilarity can be used to increase the likelihood of positive additivity. If one knows, for example, that the changes dss_034 and dss_009 (which are SNP swaps) from the top ranked strain above are on the same metabolic pathway and have similar performance characteristics, then that information could be used to select another top ranking strain with a dissimilar composition of changes. As described in the section above concerning epistasis mapping, the predicted best genetic changes may be filtered to restrict selection to mutations with sufficiently dissimilar response profiles. Alternatively, the linear regression may be a weighted least squares regression using the similarity matrix to weight predictions.

Diversity of Predicted Performance

Finally, one may choose to design strains with middling or poor predicted performance, in order to validate and subsequently improve the predictive models.

Iterative Strain Design Optimization

As described for the example above, all of the top 100 strain designs contain the changes pcg3121_pgi, pcg1860_pyc, dss_339, and pcg0007_39 lysa. Additionally, the top candidate strain design contains the changes dss_034, dss_009.

In embodiments, the order placement engine 208 places a factory order to the factory 210 to manufacture microbial strains incorporating the top candidate mutations. In feedback-loop fashion, the results may be analyzed by the analysis equipment 214 to determine which microbes exhibit desired phenotypic properties (314). During the analysis phase, the modified strain cultures are evaluated to determine their performance, i.e., their expression of desired phenotypic properties, including the ability to be produced at industrial scale. For example, the analysis phase uses, among other things, image data of plates to measure microbial colony growth as an indicator of colony health. The analysis equipment 214 is used to correlate genetic changes with phenotypic performance, and save the resulting genotype-phenotype correlation data in libraries, which may be stored in library 206, to inform future microbial production.

In particular, the candidate changes that actually result in sufficiently high measured performance may be added as rows in the database to tables such as Table 4 above. In this manner, the best performing mutations are added to the predictive strain design model in a supervised machine learning fashion.

LIMS iterates the design/build/test/analyze cycle based on the correlations developed from previous factory runs. During a subsequent cycle, the analysis equipment 214 alone, or in conjunction with human operators, may select the best candidates as base strains for input back into input interface 202, using the correlation data to fine tune genetic modifications to achieve better phenotypic performance with finer granularity. In this manner, the laboratory information management system of embodiments of the disclosure implements a quality improvement feedback loop.

In sum, with reference to the flowchart of FIG. 33 the iterative predictive strain design workflow may be described as follows:

-   -   Generate a training set of input and output variables, e.g.,         genetic changes as inputs and performance features as outputs         (3302). Generation may be performed by the analysis equipment         214 based upon previous genetic changes and the corresponding         measured performance of the microbial strains incorporating         those genetic changes.     -   Develop an initial model (e.g., linear regression model) based         upon training set (3304). This may be performed by the analysis         equipment 214.     -   Generate design candidate strains (3306)         -   In one embodiment, the analysis equipment 214 may fix the             number of genetic changes to be made to a background strain,             in the form of combinations of changes. To represent these             changes, the analysis equipment 214 may provide to the             interpreter 204 one or more DNA specification expressions             representing those combinations of changes. (These genetic             changes or the microbial strains incorporating those changes             may be referred to as “test inputs.”) The interpreter 204             interprets the one or more DNA specifications, and the             execution engine 207 executes the DNA specifications to             populate the DNA specification with resolved outputs             representing the individual candidate design strains for             those changes.     -   Based upon the model, the analysis equipment 214 predicts         expected performance of each candidate design strain (3308).     -   The analysis equipment 214 selects a limited number of candidate         designs, e.g., 100, with highest predicted performance (3310).         -   As described elsewhere herein with respect to epistasis             mapping, the analysis equipment 214 may account for             second-order effects such as epistasis, by, e.g., filtering             top designs for epistatic effects, or factoring epistasis             into the predictive model.     -   Build the filtered candidate strains (at the factory 210) based         on the factory order generated by the order placement engine 208         (3312).     -   The analysis equipment 214 measures the actual performance of         the selected strains, selects a limited number of those selected         strains based upon their superior actual performance (3314), and         adds the design changes and their resulting performance to the         predictive model (3316). In the linear regression example, add         the sets of design changes and their associated performance as         new rows in Table 4.     -   The analysis equipment 214 then iterates back to generation of         new design candidate strains (3306), and continues iterating         until a stop condition is satisfied. The stop condition may         comprise, for example, the measured performance of at least one         microbial strain satisfying a performance metric, such as yield,         growth rate, or titer.

In the example above, the iterative optimization of strain design employs feedback and linear regression to implement machine learning. In general, machine learning may be described as the optimization of performance criteria, e.g., parameters, techniques or other features, in the performance of an informational task (such as classification or regression) using a limited number of examples of labeled data, and then performing the same task on unknown data. In supervised machine learning such as that of the linear regression example above, the machine (e.g., a computing device) learns, for example, by identifying patterns, categories, statistical relationships, or other attributes, exhibited by training data. The result of the learning is then used to predict whether new data will exhibit the same patterns, categories, statistical relationships or other attributes.

Embodiments of the disclosure may employ other supervised machine learning techniques when training data is available. In the absence of training data, embodiments may employ unsupervised machine learning. Alternatively, embodiments may employ semi-supervised machine learning, using a small amount of labeled data and a large amount of unlabeled data. Embodiments may also employ feature selection to select the subset of the most relevant features to optimize performance of the machine learning model. Depending upon the type of machine learning approach selected, as alternatives or in addition to linear regression, embodiments may employ for example, logistic regression, neural networks, support vector machines (SVMs), decision trees, hidden Markov models, Bayesian networks, Gram Schmidt, reinforcement-based learning, cluster-based learning including hierarchical clustering, genetic algorithms, and any other suitable learning machines known in the art. In particular, embodiments may employ logistic regression to provide probabilities of classification (e.g., classification of genes into different functional groups) along with the classifications themselves. See, e.g., Shevade, A simple and efficient algorithm for gene selection using sparse logistic regression, Bioinformatics, Vol. 19, No. 17 2003, pp. 2246-2253, Leng, et al., Classification using functional data analysis for temporal gene expression data, Bioinformatics, Vol. 22, No. 1, Oxford University Press (2006), pp. 68-76, all of which are incorporated by reference in their entirety herein.

Embodiments may employ graphics processing unit (GPU) accelerated architectures that have found increasing popularity in performing machine learning tasks, particularly in the form known as deep neural networks (DNN). Embodiments of the disclosure may employ GPU-based machine learning, such as that described in GPU-Based Deep Learning Inference: A Performance and Power Analysis, NVidia Whitepaper, November 2015, Dahl, et al., Multi-task Neural Networks for QSAR Predictions, Dept. of Computer Science, Univ. of Toronto, June 2014 (arXiv:1406.1231 [stat.ML]), all of which are incorporated by reference in their entirety herein. Machine learning techniques applicable to embodiments of the disclosure may also be found in, among other references, Libbrecht, et al., Machine learning applications in genetics and genomics, Nature Reviews: Genetics, Vol. 16, June 2015, Kashyap, et al., Big Data Analytics in Bioinformatics: A Machine Learning Perspective, Journal of Latex Class Files, Vol. 13, No. 9, September 2014, Prompramote, et al., Machine Learning in Bioinformatics, Chapter 5 of Bioinformatics Technologies, pp. 117-153, Springer Berlin Heidelberg 2005, all of which are incorporated by reference in their entirety herein.

Iterative Predictive Strain Design: Example

The following provides an example application of the iterative predictive strain design workflow outlined above.

An initial set of training inputs and output variables was prepared. This set comprised 1864 unique engineered strains with defined genetic composition. Each strain contained between 5 and 15 engineered changes. A total of 336 unique genetic changes were present in the training.

An initial predictive computer model was developed. The implementation used a generalized linear model (Kernel Ridge Regression with 4th order polynomial kernel). The implementation models two distinct phenotypes (yield and productivity). These phenotypes were combined as weighted sum to obtain a single score for ranking, as shown below. Various model parameters, e.g. regularization factor, were tuned via k-fold cross validation over the designated training data.

The implementation does not incorporate any explicit analysis of interaction effects as described in the Epistasis Mapping section above. However, as those skilled in the art would understand, the implemented generalized linear model may capture interaction effects implicitly through the second, third and fourth order terms of the kernel.

The model was trained against the training set. The fitted model has an R² value (coefficient of determination) of 0.52 with respect to yield and an R² value of 0.67 with respect to productivity. FIG. 47 demonstrates a significant quality fitting of the yield model to the training data.

Candidate strains were generated. This example includes a serial build constraint associated with the introduction of new genetic changes to a parent strain (in this example, only one new mutation was engineered into a strain at a time). Here, candidates are not considered simply as a function of the desired number of changes. Instead, the analysis equipment 214 selected, as a starting point, a collection of previously designed strains known to have high performance metrics (“seed strains”). The analysis equipment 214 individually applied genetic changes to each of the seed strains. The introduced genetic changes did not include those already present in the seed strain. For various technical, biological or other reasons, certain mutations were explicitly required, e.g., opca_4, or explicitly excluded, e.g., dss_422. Using 166 available seed strains and the 336 changes characterized by the model, 6239 novel candidate strains were designed.

Based upon the model, the analysis equipment 214 predicted the performance of candidate strain designs. The analysis equipment 214 ranked candidates from “best” to “worst” based on predicted performance with respect to two phenotypes of interest (yield and productivity). Specifically, the analysis equipment 214 used a weighted sum to score a candidate strain: Score=0.8*yield/max(yields)+0.2*prod/max(prods), where yield represents predicted yield for the candidate strain, max(yields) represents the maximum yield over all candidate strains, prod represents productivity for the candidate strain, and max(prods) represents the maximum yield over all candidate strains.

The analysis equipment 214 generated a final set of recommendations from the ranked list of candidates by imposing both capacity constraints and operational constraints. In this example, the capacity limit was set at 48 computer-generated candidate design strains. Due to operational constraints, in this example only one seed strain was used per column of a 96-well plate. This means that after a seed strain was chosen, up to 8 changes to that strain could be built, but only 6 seed strains could be chosen in any given week.

The trained model (described above) was used to predict the expected performance (for yield and productivity) of each candidate strain. The analysis equipment 214 ranked the candidate strains using the scoring function given above. Capacity and operational constraints were applied to yield a filtered set of 48 candidate strains. This set of filtered candidate strains is depicted in FIG. 48.

Filtered candidate strains were built (at the factory 210) based on a factory order generated by the order placement engine 208 (3312). The order was based upon DNA specifications corresponding to the candidate strains.

In practice, the build process has an expected failure rate whereby a random set of strains is not built. For this build cycle, roughly 20% of the candidate strains failed build, resulting in 37 built strains.

The analysis equipment 214 was used to measure the actual yield and productivity performance of the selected strains. The analysis equipment 214 evaluated the model and recommended strains based on three criteria: model accuracy; improvement in strain performance; and equivalence (or improvement) to human expert-generated designs.

The yield and productivity phenotypes were measured for recommended strains and compared to the values predicted by the model. As shown in FIG. 49, the model demonstrates useful predictive utility. In particular, the predicted yield values for the recommended strains have a Pearson-r correlation coefficient of 0.59 with the corresponding observations.

Next, the analysis equipment 214 computed percentage performance change from the parent strain for each of the recommended strains. This data is shown in FIG. 50 (in light gray). The inventors found that many of the predicted strains in fact exhibited the expected performance gains with respect to their immediate parents. In particular, the best predicted strain showed a 6% improvement in yield with respect to its immediate parent.

In parallel with the model-based strain design process described above, a collection of 48 strains was independently designed by a human expert. Of these strains, 37 were successfully built and tested. This data demonstrated that the model-based strain designs performed comparably to strains designed by human experts. These experts are highly-skilled (e.g., Ph.D.-level) scientists employed or otherwise engaged by the assignee of the present invention, and familiar with the embodiments of this disclosure. To compare the two methods, the inventors first inspected the performance distributions of each group (FIG. 51). In this experiment, the mean yield of model-based strains showed a 1% increase with respect to human expert generated designs.

The inventors then compared human expert-designed and computer-model-designed strains grouped by background, i.e., new strains with the same parent (FIG. 52). Again, the inventors found that computer-generated designs perform comparably to, and in some cases better than, the human expert-generated designs, and further tend to produce less variability. Finally, the inventors compared the percentage change with respect to the parent strains of the human expert and model-designed strains (FIG. 50). Again, these populations showed comparable gains.

See Table 4.1 for tabulated summary statistics.

TABLE 4.1 Measured performance statistics for strains designed by the predictive model and by a human expert reference. Productivity design Yield change Productivity change from parent method Yield [AU] from parent [%] [AU] [%] computer count 37 37 37 37 model mean 1.058068108 0.3578340 0.737928919 −2.5428848 std 0.017811031 1.8293665 0.083619804 9.6743873 min 1.015310000 −4.5346677 0.572780000 −23.3626353 median 1.058710000 0.005007939 0.766870000 −1.1824159 max 1.093510000 6.0097309 0.872790000 26.6124119 Human count 37 37 37 37 expert mean 1.038804595 −0.0005237 0.748320811 −1.6126436 std 0.032053625 1.9227716 0.120527468 9.8530758 min 0.964910000 −3.1043233 0.535980000 −21.4589256 median 1.045530000 0.0449168 0.760300000 −1.9241048 max 1.094790000 7.8487174 0.984110000 21.7335193

At the conclusion of each round of the prediction→build→test cycle, the inventors were interested in evaluating the quality of the model predictions and iteratively incorporating new data into the previous model. For the former—model evaluation—the inventors focused on measuring predictive accuracy by comparing model predictions with experimental measurements. Predictive accuracy can be assessed through several methods, including a correlation coefficient indicating the strength of association between the predicted and observed values, or the root-mean-square error, which is a measure of the average model error.

Over many rounds of experimentation, model predictions may drift, and new genetic changes may be added to the training inputs to improve predictive accuracy. For this example, design changes and their resulting performance were added to the predictive model (3316).

Genomic Design and Engineering as a Service

In embodiments of the disclosure, the LIMS system software 3210 of FIG. 31 may be implemented in a cloud computing system 3202 of FIG. 32, to enable multiple users to design and build microbial strains according to embodiments of the present disclosure. FIG. 32 illustrates a cloud computing environment 3204 according to embodiments of the present disclosure. Client computers 3206, such as those illustrated in FIG. 34, access the LIMS system via a network 3208, such as the Internet. In embodiments, the LIMS system application software 3210 resides in the cloud computing system 3202. The LIMS system may employ one or more computing systems using one or more processors, of the type illustrated in FIG. 34. The cloud computing system itself includes a network interface 3212 to interface the LIMS system applications 3210 to the client computers 3206 via the network 3208. The network interface 3212 may include an application programming interface (API) to enable client applications at the client computers 3206 to access the LIMS system software 3210. In particular, through the API, client computers 3206 may access components of the LIMS system 200, including without limitation the software running the input interface 202, the interpreter 204, the execution engine 207, the order placement engine 208, the factory 210, as well as test equipment 212 and analysis equipment 214. A software as a service (SaaS) software module 3214 offers the LIMS system software 3210 as a service to the client computers 3206. A cloud management module 3216 manages access to the LIMS system 3210 by the client computers 3206. The cloud management module 3216 may enable a cloud architecture that employs multitenant applications, virtualization or other architectures known in the art to serve multiple users.

Genomic Automation

Automation of the methods of the present disclosure enables high-throughput phenotypic screening and identification of target products from multiple test strain variants simultaneously.

The aforementioned genomic engineering predictive modeling platform is premised upon the fact that hundreds and thousands of mutant strains are constructed in a high-throughput fashion. The robotic and computer systems described below are the structural mechanisms by which such a high-throughput process can be carried out.

In some embodiments, the present disclosure teaches methods of improving host cell productivities, or rehabilitating industrial strains. As part of this process, the present disclosure teaches methods of assembling DNA, building new strains, screening cultures in plates, and screening cultures in models for tank fermentation. In some embodiments, the present disclosure teaches that one or more of the aforementioned methods of creating and testing new host strains is aided by automated robotics.

In some embodiments, the present disclosure teaches a high-throughput strain engineering platform as depicted in FIG. 6.

HTP Robotic Systems

In some embodiments, the automated methods of the disclosure comprise a robotic system. The systems outlined herein are generally directed to the use of 96- or 384-well microtiter plates, but as will be appreciated by those in the art, any number of different plates or configurations may be used. In addition, any or all of the steps outlined herein may be automated; thus, for example, the systems may be completely or partially automated.

In some embodiments, the automated systems of the present disclosure comprise one or more work modules. For example, in some embodiments, the automated system of the present disclosure comprises a DNA synthesis module, a vector cloning module, a strain transformation module, a screening module, and a sequencing module (see FIG. 7).

As will be appreciated by those in the art, an automated system can include a wide variety of components, including, but not limited to: liquid handlers; one or more robotic arms; plate handlers for the positioning of microplates; plate sealers, plate piercers, automated lid handlers to remove and replace lids for wells on non-cross contamination plates; disposable tip assemblies for sample distribution with disposable tips; washable tip assemblies for sample distribution; 96 well loading blocks; integrated thermal cyclers; cooled reagent racks; microtiter plate pipette positions (optionally cooled); stacking towers for plates and tips; magnetic bead processing stations; filtrations systems; plate shakers; barcode readers and applicators; and computer systems.

In some embodiments, the robotic systems of the present disclosure include automated liquid and particle handling enabling high-throughput pipetting to perform all the steps in the process of gene targeting and recombination applications. This includes liquid and particle manipulations such as aspiration, dispensing, mixing, diluting, washing, accurate volumetric transfers; retrieving and discarding of pipette tips; and repetitive pipetting of identical volumes for multiple deliveries from a single sample aspiration. These manipulations are cross-contamination-free liquid, particle, cell, and organism transfers. The instruments perform automated replication of microplate samples to filters, membranes, and/or daughter plates, high-density transfers, full-plate serial dilutions, and high capacity operation.

In some embodiments, the customized automated liquid handling system of the disclosure is a TECAN machine (e.g. a customized TECAN Freedom Evo).

In some embodiments, the automated systems of the present disclosure are compatible with platforms for multi-well plates, deep-well plates, square well plates, reagent troughs, test tubes, mini tubes, microfuge tubes, cryovials, filters, micro array chips, optic fibers, beads, agarose and acrylamide gels, and other solid-phase matrices or platforms are accommodated on an upgradeable modular deck. In some embodiments, the automated systems of the present disclosure contain at least one modular deck for multi-position work surfaces for placing source and output samples, reagents, sample and reagent dilution, assay plates, sample and reagent reservoirs, pipette tips, and an active tip-washing station.

In some embodiments, the automated systems of the present disclosure include high-throughput electroporation systems. In some embodiments, the high-throughput electroporation systems are capable of transforming cells in 96 or 384-well plates. In some embodiments, the high-throughput electroporation systems include VWR® High-throughput Electroporation Systems, BTX™, Bio-Rad® Gene Pulser MXcell™ or other multi-well electroporation system.

In some embodiments, the integrated thermal cycler and/or thermal regulators are used for stabilizing the temperature of heat exchangers such as controlled blocks or platforms to provide accurate temperature control of incubating samples from 0° C. to 100° C.

In some embodiments, the automated systems of the present disclosure are compatible with interchangeable machine-heads (single or multi-channel) with single or multiple magnetic probes, affinity probes, replicators or pipetters, capable of robotically manipulating liquid, particles, cells, and multi-cellular organisms. Multi-well or multi-tube magnetic separators and filtration stations manipulate liquid, particles, cells, and organisms in single or multiple sample formats.

In some embodiments, the automated systems of the present disclosure are compatible with camera vision and/or spectrometer systems. Thus, in some embodiments, the automated systems of the present disclosure are capable of detecting and logging color and absorption changes in ongoing cellular cultures.

In some embodiments, the automated system of the present disclosure is designed to be flexible and adaptable with multiple hardware add-ons to allow the system to carry out multiple applications. The software program modules allow creation, modification, and running of methods. The system's diagnostic modules allow setup, instrument alignment, and motor operations. The customized tools, labware, and liquid and particle transfer patterns allow different applications to be programmed and performed. The database allows method and parameter storage. Robotic and computer interfaces allow communication between instruments.

Thus, in some embodiments, the present disclosure teaches a high-throughput strain engineering platform, as depicted in FIG. 26.

Persons having skill in the art will recognize the various robotic platforms capable of carrying out the HTP engineering methods of the present disclosure. Table 5 below provides a non-exclusive list of scientific equipment capable of carrying out each step of the HTP engineering steps of the present disclosure as described in FIG. 26.

TABLE 5 Non-exclusive list of Scientific Equipment Compatible with the HTP engineering methods of the present disclosure. Equipment Compatible Equipment Type Operation(s) performed Make/Model/Configuration Acquire and build DNA pieces liquid handlers Hitpicking (combining by Hamilton Microlab STAR, transferring) Labcyte Echo 550, Tecan EVO primers/templates for PCR 200, Beckman Coulter Biomek amplification of DNA parts FX, or equivalents Thermal cyclers PCR amplification of DNA Inheco Cycler, ABI 2720, ABI parts Proflex 384, ABI Veriti, or equivalents QC DNA parts Fragment gel electrophoresis to Agilent Bioanalyzer, AATI analyzers confirm PCR products of Fragment Analyzer, or (capillary appropriate size equivalents electrophoresis) Sequencer Verifying sequence of Beckman Ceq-8000, Beckman (sanger: parts/templates GenomeLab ™, or equivalents Beckman) NGS (next Verifying sequence of Illumina MiSeq series generation parts/templates sequences, illumina Hi-Seq, Ion sequencing) torrent, pac bio or other instrument equivalents nanodrop/plate assessing concentration of Molecular Devices SpectraMax reader DNA samples M5, Tecan M1000, or equivalents. Generate DNA liquid handlers Hitpicking (combining by Hamilton Microlab STAR, assembly transferring) DNA parts for Labcyte Echo 550, Tecan EVO assembly along with 200, Beckman Coulter Biomek cloning vector, addition of FX, or equivalents reagents for assembly reaction/process QC DNA assembly Colony pickers for inoculating colonies in Scirobotics Pickolo, Molecular liquid media Devices QPix 420 liquid handlers Hitpicking Hamilton Microlab STAR, primers/templates, diluting Labcyte Echo 550, Tecan EVO samples 200, Beckman Coulter Biomek FX, or equivalents Fragment gel electrophoresis to Agilent Bioanalyzer, AATI analyzers confirm assembled Fragment Analyzer (capillary products of appropriate electrophoresis) size Sequencer Verifying sequence of ABI3730 Thermo Fisher, (sanger: assembled plasmids Beckman Ceq-8000, Beckman Beckman) GenomeLab ™, or equivalents NGS (next Verifying sequence of Illumina MiSeq series generation assembled plasmids sequences, illumina Hi-Seq, Ion sequencing) torrent, pac bio or other instrument equivalents Prepare base strain and DNA centrifuge spinning/pelleting cells Beckman Avanti floor assembly centrifuge, Hettich Centrifuge Transform DNA into base Electroporators electroporative BTX Gemini X2, BIO-RAD strain transformation of cells MicroPulser Electroporator Ballistic ballistic transformation of BIO-RAD PDS1000 transformation cells Incubators, for chemical Inheco Cycler, ABI 2720, ABI thermal cyclers transformation/heat shock Proflex 384, ABI Veriti, or equivalents Liquid handlers for combining DNA, cells, Hamilton Microlab STAR, buffer Labcyte Echo 550, Tecan EVO 200, Beckman Coulter Biomek FX, or equivalents Integrate DNA into genome of base strain Colony pickers for inoculating colonies in Scirobotics Pickolo, Molecular liquid media Devices QPix 420 Liquid handlers For transferring cells onto Hamilton Microlab STAR, Agar, transferring from Labcyte Echo 550, Tecan EVO culture plates to different 200, Beckman Coulter Biomek culture plates (inoculation FX, or equivalents into other selective media) Platform shaker- incubation with shaking of Kuhner Shaker ISF4-X, Inforsht incubators microtiter plate cultures Multitron Pro QC transformed strain Colony pickers for inoculating colonies in Scirobotics Pickolo, Molecular liquid media Devices QPix 420 liquid handlers Hitpicking Hamilton Microlab STAR, primers/templates, diluting Labcyte Echo 550, Tecan EVO samples 200, Beckman Coulter Biomek FX, or equivalents Thermal cyclers cPCR verification of Inheco Cycler, ABI 2720, ABI strains Proflex 384, ABI Veriti, or equivalents Fragment gel electrophoresis to Infors-ht Multitron Pro, Kuhner analyzers confirm cPCR products of Shaker ISF4-X (capillary appropriate size electrophoresis) Sequencer Sequence verification of Beckman Ceq-8000, Beckman (sanger: introduced modification GenomeLab ™, or equivalents Beckman) NGS (next Sequence verification of Illumina MiSeq series generation introduced modification sequences, illumina Hi-Seq, Ion sequencing) torrent, pac bio or other instrument equivalents Select and consolidate QC'd strains into Liquid handlers For transferring from Hamilton Microlab STAR, test plate culture plates to different Labcyte Echo 550, Tecan EVO culture plates (inoculation 200, Beckman Coulter Biomek into production media) FX, or equivalents Colony pickers for inoculating colonies in Scirobotics Pickolo, Molecular liquid media Devices QPix 420 Platform shaker- incubation with shaking of Kuhner Shaker ISF4-X, Infors- incubators microtiter plate cultures ht Multitron Pro Culture strains in seed plates Liquid handlers For transferring from Hamilton Microlab STAR, culture plates to different Labcyte Echo 550, Tecan EVO culture plates (inoculation 200, Beckman Coulter Biomek into production media) FX, or equivalents Platform shaker- incubation with shaking of Kuhner Shaker ISF4-X, Infors- incubators microtiter plate cultures ht Multitron Pro liquid dispensers Dispense liquid culture Well mate (Thermo), media into microtiter plates Benchcel2R (velocity 11), plateloc (velocity 11) microplate apply barcoders to plates Microplate labeler (a2+ cab - labeler agilent), benchcell 6R (velocity 11) Generate product from strain Liquid handlers For transferring from Hamilton Microlab STAR, culture plates to different Labcyte Echo 550, Tecan EVO culture plates (inoculation 200, Beckman Coulter Biomek into production media) FX, or equivalents Platform shaker- incubation with shaking of Kuhner Shaker ISF4-X, Infors- incubators microtiter plate cultures ht Multitron Pro liquid dispensers Dispense liquid culture well mate (Thermo), media into multiple Benchcel2R (velocity 11), microtiter plates and seal plateloc (velocity 11) plates microplate Apply barcodes to plates microplate labeler (a2+ cab - labeler agilent), benchcell 6R (velocity 11) Evaluate performance Liquid handlers For processing culture Hamilton Microlab STAR, broth for downstream Labcyte Echo 550, Tecan EVO analytical 200, Beckman Coulter Biomek FX, or equivalents UHPLC, HPLC quantitative analysis of Agilent 1290 Series UHPLC precursor and target and 1200 Series HPLC with UV compounds and RI detectors, or equivalent; also any LC/MS LC/MS highly specific analysis of Agilent 6490 QQQ and 6550 precursor and target QTOF coupled to 1290 Series compounds as well as side UHPLC and degradation products Spectrophotometer Quantification of different Tecan M1000, spectramax M5, compounds using Genesys 10S spectrophotometer based assays Culture Fermenters: incubation with shaking Sartorius, DASGIPs strains in (Eppendorf), BIO-FLOs flasks (Sartorius-stedim). Applikon Platform shakers innova 4900, or any equivalent Generate product Fermenters: DASGIPs (Eppendorf), BIO-FLOs (Sartorius-stedim) from strain Evaluate performance Liquid handlers For transferring from Hamilton Microlab STAR, culture plates to different Labcyte Echo 550, Tecan EVO culture plates (inoculation 200, Beckman Coulter Biomek into production media) FX, or equivalents UHPLC, HPLC quantitative analysis of Agilent 1290 Series UHPLC precursor and target and 1200 Series HPLC with UV compounds and RI detectors, or equivalent; also any LC/MS LC/MS highly specific analysis of Agilent 6490 QQQ and 6550 precursor and target QTOF coupled to 1290 Series compounds as well as side UHPLC and degradation products Flow cytometer Characterize strain BD Accuri, Millipore Guava performance (measure viability) Spectrophotometer Characterize strain Tecan M1000, Spectramax M5, performance (measure or other equivalents biomass)

Computer System Hardware

FIG. 34 illustrates an example of a computer system 800 that may be used to execute program code stored in a non-transitory computer readable medium (e.g., memory) in accordance with embodiments of the disclosure. The computer system includes an input/output subsystem 802, which may be used to interface with human users and/or other computer systems depending upon the application. The I/O subsystem 802 may include, e.g., a keyboard, mouse, graphical user interface, touchscreen, or other interfaces for input, and, e.g., an LED or other flat screen display, or other interfaces for output, including application program interfaces (APIs). Other elements of embodiments of the disclosure, such as the components of the LIMS system, may be implemented with a computer system like that of computer system 800.

Program code may be stored in non-transitory media such as persistent storage in secondary memory 810 or main memory 808 or both. Main memory 808 may include volatile memory such as random access memory (RAM) or non-volatile memory such as read only memory (ROM), as well as different levels of cache memory for faster access to instructions and data. Secondary memory may include persistent storage such as solid state drives, hard disk drives or optical disks. One or more processors 804 reads program code from one or more non-transitory media and executes the code to enable the computer system to accomplish the methods performed by the embodiments herein. Those skilled in the art will understand that the processor(s) may ingest source code, and interpret or compile the source code into machine code that is understandable at the hardware gate level of the processor(s) 804. The processor(s) 804 may include graphics processing units (GPUs) for handling computationally intensive tasks. Particularly in machine learning, one or more CPUs 804 may offload the processing of large quantities of data to one or more GPUs 804.

The processor(s) 804 may communicate with external networks via one or more communications interfaces 807, such as a network interface card, WiFi transceiver, etc. A bus 805 communicatively couples the I/O subsystem 802, the processor(s) 804, peripheral devices 806, communications interfaces 807, memory 808, and persistent storage 810. Embodiments of the disclosure are not limited to this representative architecture. Alternative embodiments may employ different arrangements and types of components, e.g., separate buses for input-output components and memory subsystems.

Those skilled in the art will understand that some or all of the elements of embodiments of the disclosure, and their accompanying operations, may be implemented wholly or partially by one or more computer systems including one or more processors and one or more memory systems like those of computer system 800. In particular, the elements of the LIMS system 200 and any robotics and other automated systems or devices described herein may be computer-implemented. Some elements and functionality may be implemented locally and others may be implemented in a distributed fashion over a network through different servers, e.g., in client-server fashion, for example. In particular, server-side operations may be made available to multiple clients in a software as a service (SaaS) fashion, as shown in FIG. 32.

The term component in this context refers broadly to software, hardware, or firmware (or any combination thereof) component. Components are typically functional components that can generate useful data or other output using specified input(s). A component may or may not be self-contained. An application program (also called an “application”) may include one or more components, or a component can include one or more application programs.

Some embodiments include some, all, or none of the components along with other modules or application components. Still yet, various embodiments may incorporate two or more of these components into a single module and/or associate a portion of the functionality of one or more of these components with a different component.

The term “memory” can be any device or mechanism used for storing information. In accordance with some embodiments of the present disclosure, memory is intended to encompass any type of, but is not limited to: volatile memory, nonvolatile memory, and dynamic memory. For example, memory can be random access memory, memory storage devices, optical memory devices, magnetic media, floppy disks, magnetic tapes, hard drives, SIMMs, SDRAM, DIMMs, RDRAM, DDR RAM, SODIMMS, erasable programmable read-only memories (EPROMs), electrically erasable programmable read-only memories (EEPROMs), compact disks, DVDs, and/or the like. In accordance with some embodiments, memory may include one or more disk drives, flash drives, databases, local cache memories, processor cache memories, relational databases, flat databases, servers, cloud based platforms, and/or the like. In addition, those of ordinary skill in the art will appreciate many additional devices and techniques for storing information can be used as memory.

Memory may be used to store instructions for running one or more applications or modules on a processor. For example, memory could be used in some embodiments to house all or some of the instructions needed to execute the functionality of one or more of the modules and/or applications disclosed in this application.

HTP Microbial Strain Engineering Based Upon Genetic Design Predictions: an Example Workflow

In some embodiments, the present disclosure teaches the directed engineering of new host organisms based on the recommendations of the computational analysis systems of the present disclosure.

In some embodiments, the present disclosure is compatible with all genetic design and cloning methods. That is, in some embodiments, the present disclosure teaches the use of traditional cloning techniques such as polymerase chain reaction, restriction enzyme digestions, ligation, homologous recombination, RT PCR, and others generally known in the art and are disclosed in for example: Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual (3^(rd) ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.), incorporated herein by reference.

In some embodiments, the cloned sequences can include possibilities from any of the HTP genetic design libraries taught herein, for example: promoters from a promoter swap library, SNPs from a SNP swap library, start or stop codons from a start/stop codon exchange library, terminators from a STOP swap library, or sequence optimizations from a sequence optimization library.

Further, the exact sequence combinations that should be included in a particular construct can be informed by the epistatic mapping function.

In other embodiments, the cloned sequences can also include sequences based on rational design (hypothesis-driven) and/or sequences based on other sources, such as scientific publications.

In some embodiments, the present disclosure teaches methods of directed engineering, including the steps of i) generating custom-made SNP-specific DNA, ii) assembling SNP-specific plasmids, iii) transforming target host cells with SNP-specific DNA, and iv) looping out any selection markers (See FIG. 2).

FIG. 6A depicts the general workflow of the strain engineering methods of the present disclosure, including acquiring and assembling DNA, assembling vectors, transforming host cells and removing selection markers.

Build Specific DNA Oligonucleotides

In some embodiments, the present disclosure teaches inserting and/or replacing and/or altering and/or deleting a DNA segment of the host cell organism. In some aspects, the methods taught herein involve building an oligonucleotide of interest (i.e. a target DNA segment), that will be incorporated into the genome of a host organism. In some embodiments, the target DNA segments of the present disclosure can be obtained via any method known in the art, including: copying or cutting from a known template, mutation, or DNA synthesis. In some embodiments, the present disclosure is compatible with commercially available gene synthesis products for producing target DNA sequences (e.g., GeneArt™, GeneMaker™, GenScript™, Anagen™, Blue Heron™, Entelechon™, GeNOsys, Inc., or Qiagen™).

In some embodiments, the target DNA segment is designed to incorporate a SNP into a selected DNA region of the host organism (e.g., adding a beneficial SNP). In other embodiments, the DNA segment is designed to remove a SNP from the DNA of the host organisms (e.g., removing a detrimental or neutral SNP).

In some embodiments, the oligonucleotides used in the inventive methods can be synthesized using any of the methods of enzymatic or chemical synthesis known in the art. The oligonucleotides may be synthesized on solid supports such as controlled pore glass (CPG), polystyrene beads, or membranes composed of thermoplastic polymers that may contain CPG. Oligonucleotides can also be synthesized on arrays, on a parallel microscale using microfluidics (Tian et al., Mol. BioSyst., 5, 714-722 (2009)), or known technologies that offer combinations of both (see Jacobsen et al., U.S. Pat. App. No. 2011/0172127).

Synthesis on arrays or through microfluidics offers an advantage over conventional solid support synthesis by reducing costs through lower reagent use. The scale required for gene synthesis is low, so the scale of oligonucleotide product synthesized from arrays or through microfluidics is acceptable. However, the synthesized oligonucleotides are of lesser quality than when using solid support synthesis (See Tian infra.; see also Staehler et al., U.S. Pat. App. No. 2010/0216648).

A great number of advances have been achieved in the traditional four-step phosphoramidite chemistry since it was first described in the 1980s (see for example, Sierzchala, et al. J. Am. Chem. Soc., 125, 13427-13441 (2003) using peroxy anion deprotection; Hayakawa et al., U.S. Pat. No. 6,040,439 for alternative protecting groups; Azhayev et al, Tetrahedron 57, 4977-4986 (2001) for universal supports; Kozlov et al., Nucleosides, Nucleotides, and Nucleic Acids, 24 (5-7), 1037-1041 (2005) for improved synthesis of longer oligonucleotides through the use of large-pore CPG; and Damha et al., NAR, 18, 3813-3821 (1990) for improved derivatization).

Regardless of the type of synthesis, the resulting oligonucleotides may then form the smaller building blocks for longer oligonucleotides. In some embodiments, smaller oligonucleotides can be joined together using protocols known in the art, such as polymerase chain assembly (PCA), ligase chain reaction (LCR), and thermodynamically balanced inside-out synthesis (TBIO) (see Czar et al. Trends in Biotechnology, 27, 63-71 (2009)). In PCA, oligonucleotides spanning the entire length of the desired longer product are annealed and extended in multiple cycles (typically about 55 cycles) to eventually achieve full-length product. LCR uses ligase enzyme to join two oligonucleotides that are both annealed to a third oligonucleotide. TBIO synthesis starts at the center of the desired product and is progressively extended in both directions by using overlapping oligonucleotides that are homologous to the forward strand at the 5′ end of the gene and against the reverse strand at the 3′ end of the gene.

Another method of synthesizing a larger double stranded DNA fragment is to combine smaller oligonucleotides through top-strand PCR (TSP). In this method, a plurality of oligonucleotides spans the entire length of a desired product and contain overlapping regions to the adjacent oligonucleotide(s). Amplification can be performed with universal forward and reverse primers, and through multiple cycles of amplification a full-length double stranded DNA product is formed. This product can then undergo optional error correction and further amplification that results in the desired double stranded DNA fragment end product.

In one method of TSP, the set of smaller oligonucleotides that will be combined to form the full-length desired product are between 40-200 bases long and overlap each other by at least about 15-20 bases. For practical purposes, the overlap region should be at a minimum long enough to ensure specific annealing of oligonucleotides and have a high enough melting temperature (Tm) to anneal at the reaction temperature employed. The overlap can extend to the point where a given oligonucleotide is completely overlapped by adjacent oligonucleotides. The amount of overlap does not seem to have any effect on the quality of the final product. The first and last oligonucleotide building block in the assembly should contain binding sites for forward and reverse amplification primers. In one embodiment, the terminal end sequence of the first and last oligonucleotide contain the same sequence of complementarity to allow for the use of universal primers.

Assembling/Cloning Custom Plasmids

In some embodiments, the present disclosure teaches methods for constructing vectors capable of inserting desired target DNA sections (e.g. containing a particular SNP) into the genome of host organisms. In some embodiments, the present disclosure teaches methods of cloning vectors comprising the target DNA, homology arms, and at least one selection marker (see FIG. 3).

In some embodiments, the present disclosure is compatible with any vector suited for transformation into the host organism. In some embodiments, the present disclosure teaches use of shuttle vectors compatible with a host cell. In one embodiment, a shuttle vector for use in the methods provided herein is a shuttle vector compatible with an E. coli and/or Corynebacterium host cell. Shuttle vectors for use in the methods provided herein can comprise markers for selection and/or counter-selection as described herein. The markers can be any markers known in the art and/or provided herein. The shuttle vectors can further comprise any regulatory sequence(s) and/or sequences useful in the assembly of said shuttle vectors as known in the art. The shuttle vectors can further comprise any origins of replication that may be needed for propagation in a host cell as provided herein such as, for example, E. coli or C. glutanicum. The regulatory sequence can be any regulatory sequence known in the art or provided herein such as, for example, a promoter, start, stop, signal, secretion and/or termination sequence used by the genetic machinery of the host cell. In certain instances, the target DNA can be inserted into vectors, constructs or plasmids obtainable from any repository or catalogue product, such as a commercial vector (see e.g., DNA2.0 custom or GATEWAY® vectors). In certain instances, the target DNA can be inserted into vectors, constructs or plasmids obtainable from any repository or catalogue product, such as a commercial vector (see e.g., DNA2.0 custom or GATEWAY® vectors).

In some embodiments, the assembly/cloning methods of the present disclosure may employ at least one of the following assembly strategies: 1) type II conventional cloning, ii) type II S-mediated or “Golden Gate” cloning (see, e.g., Engler, C., R. Kandzia, and S. Marillonnet. 2008 “A one pot, one step, precision cloning method with high-throughput capability”. PLos One 3:e3647; Kotera, I., and T. Nagai. 2008 “A high-throughput and single-tube recombination of crude PCR products using a DNA polymerase inhibitor and type IIS restriction enzyme.” J Biotechnol 137:1-7.; Weber, E., R. Gruetzner, S. Werner, C. Engler, and S. Marillonnet. 2011 Assembly of Designer TAL Effectors by Golden Gate Cloning. PloS One 6:e19722), iii) GATEWAY® recombination, iv) TOPO® cloning, exonuclease-mediated assembly (Aslanidis and de Jong 1990. “Ligation-independent cloning of PCR products (LIC-PCR).” Nucleic Acids Research, Vol. 18, No. 20 6069), v) homologous recombination, vi) non-homologous end joining, vii) Gibson assembly (Gibson et al., 2009 “Enzymatic assembly of DNA molecules up to several hundred kilobases” Nature Methods 6, 343-345) or a combination thereof. Modular type IIS based assembly strategies are disclosed in PCT Publication WO 2011/154147, the disclosure of which is incorporated herein by reference.

In some embodiments, the present disclosure teaches cloning vectors with at least one selection marker. Various selection marker genes are known in the art often encoding antibiotic resistance function for selection in prokaryotic (e.g., against ampicillin, kanamycin, tetracycline, chloramphenicol, zeocin, spectinomycin/streptomycin) or eukaryotic cells (e.g. geneticin, neomycin, hygromycin, puromycin, blasticidin, zeocin) under selective pressure. Other marker systems allow for screening and identification of wanted or unwanted cells such as the well-known blue/white screening system used in bacteria to select positive clones in the presence of X-gal or fluorescent reporters such as green or red fluorescent proteins expressed in successfully transduced host cells. Another class of selection markers most of which are only functional in prokaryotic systems relates to counter selectable marker genes often also referred to as “death genes” which express toxic gene products that kill producer cells. Examples of such genes include sacB, rpsL(strA), tetAR, pheS, thyA, gata-1, or ccdB, the function of which is described in (Reyrat et al. 1998 “Counterselectable Markers: Untapped Tools for Bacterial Genetics and Pathogenesis.” Infect Immun. 66(9): 4011-4017).

Protoplasting Methods

In one embodiment, the methods and systems provided herein make use of the generation of protoplasts from filamentous fungal cells. Suitable procedures for preparation of protoplasts can be any known in the art including, for example, those described in EP 238,023 and Yelton et al. (1984, Proc. Natl. Acad. Sci. USA 81:1470-1474). In one embodiment, protoplasts are generated by treating a culture of filamentous fungal cells with one or more lytic enzymes or a mixture thereof. The lytic enzymes can be a beta-glucanase and/or a polygalacturonase. In one embodiment, the enzyme mixture for generating protoplasts is VinoTaste concentrate. Following enzymatic treatment, the protoplasts can be isolated using methods known in the art such as, for example, centrifugation.

The pre-cultivation and the actual protoplasting step can be varied to optimize the number of protoplasts and the transformation efficiency. For example, there can be variations of inoculum size, inoculum method, pre-cultivation media, pre-cultivation times, pre-cultivation temperatures, mixing conditions, washing buffer composition, dilution ratios, buffer composition during lytic enzyme treatment, the type and/or concentration of lytic enzyme used, the time of incubation with lytic enzyme, the protoplast washing procedures and/or buffers, the concentration of protoplasts and/or polynucleotide and/or transformation reagents during the actual transformation, the physical parameters during the transformation, the procedures following the transformation up to the obtained transformants.

Protoplasts can be resuspended in an osmotic stabilizing buffer. The composition of such buffers can vary depending on the species, application and needs. However, typically these buffers contain either an organic component like sucrose, citrate, mannitol or sorbitol between 0.5 and 2 M. More preferably between 0.75 and 1.5 M; most preferred is 1 M. Otherwise these buffers contain an inorganic osmotic stabilizing component like KCl, MgSO.sub.4, NaCl or MgCl.sub.2 in concentrations between 0.1 and 1.5 M. Preferably between 0.2 and 0.8 M; more preferably between 0.3 and 0.6 M, most preferably 0.4 M. The most preferred stabilizing buffers are STC (sorbitol, 0.8 M; CaCl.sub.2, 25 mM; Tris, 25 mM; pH 8.0) or KCl-citrate (KCl, 0.3-0.6 M; citrate, 0.2% (w/v)). The protoplasts can be used in a concentration between 1×10⁵ and 1×10¹⁰ cells/ml. Preferably, the concentration is between 1×10⁶ and 1×10⁹; more preferably the concentration is between 1×10⁷ and 5×10⁸; most preferably the concentration is 1×10⁸ cells/ml. DNA is used in a concentration between 0.01 and 10 ug; preferably between 0.1 and 5 ug, even more preferably between 0.25 and 2 ug; most preferably between 0.5 and 1 ug. To increase the efficiency of transfection carrier DNA (as salmon sperm DNA or non-coding vector DNA) may be added to the transformation mixture.

In one embodiment, following generation and subsequent isolation, the protoplasts are mixed with one or more cryoprotectants. The cryoprotectants can be glycols, dimethyl sulfoxide (DMSO), polyols, sugars, 2-Methyl-2,4-pentanediol (MPD), polyvinylpyrrolidone (PVP), methylcellulose, C-linked antifreeze glycoproteins (C-AFGP) or combinations thereof. Glycols for use as cryoprotectants in the methods and systems provided herein can be selected from ethylene glycol, propylene glycol, polypropylene glycol (PEG), glycerol, or combinations thereof. Polyols for use as cryoprotectants in the methods and systems provided herein can be selected from propane-1,2-diol, propane-1,3-diol, 1,1,1-tris-(hydroxymethyl)ethane (THME), and 2-ethyl-2-(hydroxymethyl)-propane-1,3-diol (EHMP), or combinations thereof. Sugars for use as cryoprotectants in the methods and systems provided herein can be selected from trehalose, sucrose, glucose, raffinose, dextrose or combinations thereof. In one embodiment, the protoplasts are mixed with DMSO. DMSO can be mixed with the protoplasts at a final concentration of at least, at most, less than, greater than, equal to, or about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 12.5%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, or 75% w/v or v/v. The protoplasts/cryoprotectant (e.g., DMSO) mixture can be distributed to microtiter plates prior to storage. The protoplast/cryoprotectant (e.g., DMSO) mixture can be stored at any temperature provided herein for long-term storage (e.g., several hours, day(s), week(s), month(s), year(s)) as provided herein such as, for example −20° C. or −80° C. In one embodiment, an additional cryoprotectant (e.g., PEG) is added to the protoplasts/DMSO mixture. In yet another embodiment, the additional cryoprotectant (e.g., PEG) is added to the protoplast/DMSO mixture prior to storage. The PEG can be any PEG provided herein and can be added at any concentration (e.g., w/v or v/v) as provided herein.

Protoplast Transformation Methods

In one embodiment, the methods and systems provided herein require the transfer of nucleic acids to protoplasts derived from filamentous fungal cells as described herein. In another embodiment, the transformation utilized by the methods and systems provided herein is high-throughput in nature and/or is partially or fully automated as described herein. Further to this embodiment, the transformation is performed by adding constructs or expression constructs as described herein to the wells of a microtiter plate followed by aliquoting protoplasts generated by the methods provided herein to each well of the microtiter plate. Suitable procedures for transformation/transfection of protoplasts can be any known in the art including, for example, those described in international patent applications PCT/NL99/00618, PCT/EP99/202516, Finkelstein and Ball (eds.), Biotechnology of filamentous fungi, technology and products, Butterworth-Heinemann (1992), Bennett and Lasure (eds.) More Gene Manipulations in fungi, Academic Press (1991), Turner, in: Puhler (ed), Biotechnology, second completely revised edition, VHC (1992) protoplast fusion, and the Ca-PEG mediated protoplast transformation as described in EP635574B. Alternatively, transformation of the filamentous fungal host cells or protoplasts derived therefrom can also be performed by electroporation such as, for example, the electroporation described by Chakraborty and Kapoor, Nucleic Acids Res. 18:6737 (1990), Agrobacterium tumefaciens-mediated transformation, biolistic introduction of DNA such as, for example, as described in Christiansen et al., Curr. Genet. 29:100 102 (1995); Durand et al., Curr. Genet. 31:158 161 (1997); and Barcellos et al., Can. J. Microbiol. 44:1137 1141 (1998) or “magneto-biolistic” transfection of cells such as, for example, described in U.S. Pat. Nos. 5,516,670 and 5,753,477. In one embodiment, the transformation procedure used in the methods and systems provided herein is one amendable to being high-throughput and/or automated as provided herein such as, for example, PEG mediated transformation.

Transformation of the protoplasts generated using the methods described herein can be facilitated through the use of any transformation reagent known in the art. Suitable transformation reagents can be selected from Polyethylene Glycol (PEG), FUGENE® HD (from Roche), Lipofectamine® or OLIGOFECTAMINE® (from Invitrogen), TRANSPASS® D1 (from New England Biolabs), LYPOVEC® or LIPOGEN® (from Invivogen). In one embodiment, PEG is the most preferred transformation/transfection reagent. PEG is available at different molecular weights and can be used at different concentrations. Preferably PEG 4000 is used between 10% and 60%, more preferably between 20% and 50%, most preferably at 30%. In one embodiment, the PEG is added to the protoplasts prior to storage as described herein.

Transformation of Host Cells

In some embodiments, the vectors of the present disclosure may be introduced into the host cells using any of a variety of techniques, including transformation, transfection, transduction, viral infection, gene guns, or Ti-mediated gene transfer (see Christie, P. J., and Gordon, J. E., 2014 “The Agrobacterium Ti Plasmids” Microbiol SPectr. 2014; 2(6); 10.1128). Particular methods include calcium phosphate transfection, DEAE-Dextran mediated transfection, lipofection, or electroporation (Davis, L., Dibner, M., Battey, I., 1986 “Basic Methods in Molecular Biology”). Other methods of transformation include for example, lithium acetate transformation and electroporation See, e.g., Gietz et al., Nucleic Acids Res. 27:69-74 (1992); Ito et al., J. Bacterol. 153:163-168 (1983); and Becker and Guarente, Methods in Enzymology 194:182-187 (1991). In some embodiments, transformed host cells are referred to as recombinant host strains.

In some embodiments, the present disclosure teaches high-throughput transformation of cells using the 96-well plate robotics platform and liquid handling machines of the present disclosure.

In some embodiments, the present disclosure teaches screening transformed cells with one or more selection markers as described above. In one such embodiment, cells transformed with a vector comprising a kanamycin resistance marker (KanR) are plated on media containing effective amounts of the kanamycin antibiotic. Colony forming units visible on kanamycin-laced media are presumed to have incorporated the vector cassette into their genome. Insertion of the desired sequences can be confirmed via PCR, restriction enzyme analysis, and/or sequencing of the relevant insertion site.

Looping Out of Selected Sequences

In some embodiments, the present disclosure teaches methods of looping out selected regions of DNA from the host organisms. The looping out method can be as described in Nakashima et al. 2014 “Bacterial Cellular Engineering by Genome Editing and Gene Silencing.” Int. J. Mol. Sci. 15(2), 2773-2793. In some embodiments, the present disclosure teaches looping out selection markers from positive transformants. Looping out deletion techniques are known in the art, and are described in (Tear et al. 2014 “Excision of Unstable Artificial Gene-Specific inverted Repeats Mediates Scar-Free Gene Deletions in Escherichia coli.” Appl. Biochem. Biotech. 175:1858-1867). The looping out methods used in the methods provided herein can be performed using single-crossover homologous recombination or double-crossover homologous recombination. In one embodiment, looping out of selected regions as described herein can entail using single-crossover homologous recombination as described herein.

First, loop out vectors are inserted into selected target regions within the genome of the host organism (e.g., via homologous recombination, CRISPR, or other gene editing technique). In one embodiment, single-crossover homologous recombination is used between a circular plasmid or vector and the host cell genome in order to loop-in the circular plasmid or vector such as depicted in FIG. 3. The inserted vector can be designed with a sequence which is a direct repeat of an existing or introduced nearby host sequence, such that the direct repeats flank the region of DNA slated for looping and deletion. Once inserted, cells containing the loop out plasmid or vector can be counter selected for deletion of the selection region (e.g., see FIG. 4; lack of resistance to the selection gene).

Persons having skill in the art will recognize that the description of the loopout procedure represents but one illustrative method for deleting unwanted regions from a genome. Indeed the methods of the present disclosure are compatible with any method for genome deletions, including but not limited to gene editing via CRISPR, TALENS, FOK, or other endonucleases. Persons skilled in the art will also recognize the ability to replace unwanted regions of the genome via homologous recombination techniques

EXAMPLES

The following examples are given for the purpose of illustrating various embodiments of the disclosure and are not meant to limit the present disclosure in any fashion. Changes therein and other uses which are encompassed within the spirit of the disclosure, as defined by the scope of the claims, will be recognized by those skilled in the art.

A brief table of contents is provided below solely for the purpose of assisting the reader. Nothing in this table of contents is meant to limit the scope of the examples or disclosure of the application.

TABLE 5.1 Table of Contents For Example Section. Example # Title Brief Description 1 HTP Transformation of Corynebacterium & Describes embodiments of the high Demonstration of SNP Library Creation throughput genetic engineering methods of the present disclosure. 2 HTP Genomic Engineering - Implementation Describes approaches for of a SNP Library to Rehabilitate/Improve an rehabilitating industrial organisms Industrial Microbial Strain through SNP swap methods of the present disclosure. 3 HTP Genomic Engineering - Implementation Describes an implementation of of a SNP Swap Library to Improve Strain SNP swap techniques for Performance in Lysine Production in improving the performance of Corynebacterium. Corynebacterium strain producing lysine. Also discloses selected second and third order mutation consolidations. 4 HTP Genomic Engineering - Implementation Describes methods for improving of a Promoter Swap Library to Improve an the strain performance of host Industrial Microbial Strain organisms through PRO swap genetic design libraries of the present disclosure. 5 HTP Genomic Engineering - Implementation Describes an implementation of of a PRO Swap Library to Improve Strain PRO swap techniques for Performance for Lysine Production improving the performance of Corynebacterium strain producing lysine. 6 Epistasis Mapping - An Algorithmic Tool for Describes an embodiment of the Predicting Beneficial Mutation automated tools/algorithms of the Consolidations present disclosure for predicting beneficial gene mutation consolidations. 7 HTP Genomic Engineering - PRO Swap Describes and illustrates the ability Mutation Consolidation and Multi-Factor of the HTP methods of the present Combinatorial Testing disclosure to effectively explore the large solution space created by the combinatorial consolidation of multiple gene/genetic design library combinations. 8 HTP Genomic Engineering - Implementation Describes and illustrates an of a Terminator Library to Improve an application of the STOP swap Industrial Host Strain genetic design libraries of the present disclosure. 9 Comparing HTP Toolsets vs. Traditional UV Provides experimental results Mutations. comparing the HTP genetic design methods of the present disclosure vs. traditional mutational strain improvement programs. 10 Application of HTP Engineering Methods in Describes embodiments of the high Eukaryotes throughput genetic engineering methods of the present disclosure, as applied to eukaryotic host cells. 11 HTP Genomic Engineering - Implementation Describes approaches for of an HTP SNP Library Strain Improvement rehabilitating industrial Program to Improve Citric Acid production in eukaryotic organisms through Eukaryote Aspergillus niger ATCC11414 SNP swap methods of the present disclosure.

Example 1: HTP Transformation of Corynebacterium & Demonstration of SNP Library Creation

This example illustrates embodiments of the HTP genetic engineering methods of the present disclosure. Host cells are transformed with a variety of SNP sequences of different sizes, all targeting different areas of the genome. The results demonstrate that the methods of the present disclosure are able to generate rapid genetic changes of any kind, across the entire genome of a host cell.

A. Cloning of Transformation Vectors

A variety of SNPs were chosen at random from Corynebacterium glutamicum (ATCC21300) and were cloned into Corynebacterium cloning vectors using yeast homologous recombination cloning techniques to assemble a vector in which each SNP was flanked by direct repeat regions, as described supra in the “Assembling/Cloning Custom Plasmids” section, and as illustrated in FIG. 3.

The SNP cassettes for this example were designed to include a range of homology direct repeat arm lengths ranging from 0.5 Kb, 1 Kb, 2 Kb, and 5 Kb. Moreover, SNP cassettes were designed for homologous recombination targeted to various distinct regions of the genome, as described in more detail below.

The C. glutamicum genome is 3,282,708 bp in size (see FIG. 9). The genome was arbitrarily divided into 24 equal-sized genetic regions, and SNP cassettes were designed to target each of the 24 regions. Thus, a total of 96 distinct plasmids were cloned for this Example (4 different insert sizes×24 distinct genomic regions).

Each DNA insert was produced by PCR amplification of homologous regions using commercially sourced oligos and the host strain genomic DNA described above as template. The SNP to be introduced into the genome was encoded in the oligo tails. PCR fragments were assembled into the vector backbone using homologous recombination in yeast.

Cloning of each SNP and homology arm into the vector was conducted according to the HTP engineering workflow described in FIG. 6, FIG. 3, and Table 5.

B. Transformation of Assembled Clones into E. coli

Vectors were initially transformed into E. coli using standard heat shock transformation techniques in order to identify correctly assembled clones, and to amplify vector DNA for Corynebacterium transformation.

For example, transformed E. coli bacteria were tested for assembly success. Four colonies from each E. coli transformation plate were cultured and tested for correct assembly via PCR. This process was repeated for each of the 24 transformation locations and for each of the 4 different insert sizes (i.e., for all 96 transformants of this example). Results from this experiment were represented as the number of correct colonies identified out of the four colonies that were tested for each treatment (insert size and genomic location) (see FIG. 12). Longer 5 kb inserts exhibited a decrease in assembly efficiency compared to shorter counterparts (n=96).

C. Transformation of Assembled Clones into Corynebacterium

Validated clones were transformed into Corynebacterium glutamicum host cells via electroporation. For each transformation, the number of Colony Forming Units (CFUs) per μg of DNA was determined as a function of the insert size (see FIG. 13). Coryne genome integration was also analyzed as a function of homology arm length, and the results showed that shorter arms had a lower efficiency (see FIG. 13).

Genomic integration efficiency was also analyzed with respect to the targeted genome location in C. glutamicum transformants. Genomic positions 1 and 2 exhibited slightly lowered integration efficiency compared to the rest of the genome (see FIG. 10).

D. Looping Out Selection Markers

Cultures of Corynebacterium identified as having successful integrations of the insert cassette were cultured on media containing 5% sucrose to counter select for loop outs of the sacb selection gene. Sucrose resistance frequency for various homology direct repeat arms did not vary significantly with arm length (see FIG. 14). These results suggested that loopout efficiencies remained steady across homology arm lengths of 0.5 kb to 5 kb.

In order to further validate loop out events, colonies exhibiting sucrose resistance were cultured and analyzed via sequencing.

The results for the sequencing of the insert genomic regions are summarized in Table 6 below.

TABLE 6 Loop-out Validation Frequency Outcome Frequency (sampling error 95% confidence) Successful 13% (9%/20%)  Loop out Loop Still 42% (34%/50%) present Mixed read 44% (36%/52%)

Sequencing results showed a 10-20% efficiency in loop outs. Actual loop-out probably is somewhat dependent on insert sequence. However, picking 10-20 sucrose-resistant colonies leads to high success rates.

E. Summary

Table 7 below provides a quantitative assessment of the efficiencies of the HTP genome engineering methods of the present invention. Construct assembly rates for yeast homology methodologies yielded expected DNA constructs in nearly 9 out of 10 tested colonies. Coryne transformations of SNP constructs with 2 kb homology arms yielded an average of 51 colony forming units per micro gram of DNA (CFU/μg), with 98% of said colonies exhibiting correctly integrated SNP inserts (targeting efficiency). Loop out efficiencies remained at 0.2% of cells becoming resistant when exposed to sucrose, with 13% of these exhibiting correctly looped out sequences.

TABLE 7 Summary Results for Corynebacterium glutamicum Strain Engineering Results for 2 kb Homology QC Step Arms Construct Assembly Success 87% Coryne Transformation efficiency 51 CFU/μg DNA (+/−15) Targeting efficiency 98% Loop out Efficiency 0.2% (+/−0.03%)

Example 2: HTP Genomic Engineering—Implementation of a SNP Library to Rehabilitate/Improve an Industrial Microbial Strain

This example illustrates several aspects of the SNP swap libraries of the HTP strain improvement programs of the present disclosure. Specifically, the example illustrates several envisioned approaches for rehabilitating currently existing industrial strains. This example describes the wave up and wave down approaches to exploring the phenotypic solution space created by the multiple genetic differences that may be present between “base,” “intermediate,” and industrial strains.

A. Identification of SNPs in Diversity Pool

An exemplary strain improvement program using the methods of the present disclosure was conducted on an industrial production microbial strain, herein referred to as “C.” The diversity pool strains for this program are represented by A, B, and C. Strain A represented the original production host strain, prior to any mutagenesis. Strain C represented the current industrial strain, which has undergone many years of mutagenesis and selection via traditional strain improvement programs. Strain B represented a “middle ground” strain, which had undergone some mutagenesis, and had been the predecessor of strain C. (see FIG. 17A).

Strains A, B, and C were sequenced and their genomes were analyzed for genetic differences between strains. A total of 332 non-synonymous SNPs were identified. Of these, 133 SNPs were unique to C, 153 were additionally shared by B and C, and 46 were unique to strain B (see FIG. 17B). These SNPs will be used as the diversity pool for downstream strain improvement cycles.

B. SNP Swapping Analysis

SNPs identified from the diversity pool in Part A of Example 2 will be analyzed to determine their effect on host cell performance. The initial “learning” round of the strain performance will be broken down into six steps as described below, and diagramed in FIG. 18.

First, all the SNPs from C will be individually and/or combinatorially cloned into the base A strain. This will represent a minimum of 286 individual transformants. The purpose of these transformants will be to identify beneficial SNPs.

Second, all the SNPs from C will be individually and/or combinatorially removed from the commercial strain C. This will represent a minimum of 286 individual transformants. The purpose of these transformants will be to identify neutral and detrimental SNPs. Additional optional steps 3-6 are also described below. The first and second steps of adding and subtracting SNPS from two genetic time points (base strain A, and industrial strain C) is herein referred to as “wave,” which comprises a “wave up” (addition of SNPs to a base strain, first step), and a “wave down” (removal of SNPs from the industrial strain, second step). The wave concept extends to further additions/subtractions of SNPS.

Third, all the SNPs from B will be individually and/or combinatorially cloned into the base A strain. This will represent a minimum of 199 individual transformants. The purpose of these transformants will be to identify beneficial SNPs. Several of the transformants will also serve as validation data for transformants produced in the first step.

Fourth, all the SNPs from B will be individually and/or combinatorially removed from the commercial strain B. This will represent a minimum of 199 individual transformants. The purpose of these transformants will be to identify neutral and detrimental SNPs. Several of the transformants will also serve as validation data for transformants produced in the second step.

Fifth, all the SNPs unique to C (i.e., not also present in B) will be individually and/or combinatorially cloned into the commercial B strain. This will represent a minimum of 46 individual transformants. The purpose of these transformants will be to identify beneficial SNPs. Several of the transformants will also serve as validation data for transformants produced in the first and third steps.

Sixth, all the SNPs unique to C will be individually and/or combinatorially removed from the commercial strain C. This will represent a minimum of 46 individual transformants. The purpose of these transformants will be to identify neutral and detrimental SNPs. Several of the transformants will also serve as validation data for transformants produced in the second and fourth steps.

Data collected from each of these steps is used to classify each SNP as prima facie beneficial, neutral, or detrimental.

C. Utilization of Epistatic Mapping to Determine Beneficial SNP Combinations

Beneficial SNPs identified in Part B of Example 2 will be analyzed via the epistasis mapping methods of the present disclosure, in order to identify SNPs that are likely to improve host performance when combined.

New engineered strain variants will be created using the engineering methods of Example 1 to test SNP combinations according to epistasis mapping predictions. SNPs consolidation may take place sequentially, or may alternatively take place across multiple branches such that more than one improved strain may exist with a subset of beneficial SNPs. SNP consolidation will continue over multiple strain improvement rounds, until a final strain is produced containing the optimum combination of beneficial SNPs, without any of the neutral or detrimental SNP baggage

Example 3: HTP Genomic Engineering—Implementation of a SNP Swap Library to Improve Strain Performance in Lysine Production in Corynebacterium

This example provides an illustrative implementation of a portion of the SNP Swap HTP design strain improvement program of Example 2 with the goal of producing yield and productivity improvements of lysine production in Corynebacterium.

Section B of this example further illustrates the mutation consolidation steps of the HTP strain improvement program of the present disclosure. The example thus provides experimental results for a first, second, and third round consolidation of the HTP strain improvement methods of the present disclosure.

Mutations for the second and third round consolidations are derived from separate genetic library swaps. These results thus also illustrate the ability for the HTP strain programs to be carried out multi-branch parallel tracks, and the “memory” of beneficial mutations that can be embedded into meta data associated with the various forms of the genetic design libraries of the present disclosure.

As described above, the genomes of a provided base reference strain (Strain A), and a second “engineered” strain (Strain C) were sequenced, and all genetic differences were identified. The base strain was a Corynebacterium glutamicum variant that had not undergone UV mutagenesis. The engineered strain was also a C. glutamicum strain that had been produced from the base strain after several rounds of traditional mutation improvement programs. This Example provides the SNP Swap results for 186 distinct non-synonymous SNP differences identified between strains A and C.

A. HTP Engineering and High Throughput Screening

Each of the 186 identified SNPs were individually added back into the base strain, according to the cloning and transformation methods of the present disclosure. Each newly created strain comprising a single SNP was tested for lysine yield in small scale cultures designed to assess product titer performance. Small scale cultures were conducted using media from industrial scale cultures. Product titer was optically measured at carbon exhaustion (i.e., representative of single batch yield) with a standard colorimetric assay. Briefly, a concentrated assay mixture was prepared and was added to fermentation samples such that final concentrations of reagents were 160 mM sodium phosphate buffer, 0.2 mM Amplex Red, 0.2 U/mL Horseradish Peroxidase and 0.005 U/mL of lysine oxidase. Reactions were allowed to proceed to an end point and optical density measured using a Tecan M1000 plate spectrophotometer at a 560 nm wavelength. The results of the experiment are summarized in Table 8 below, and depicted in FIG. 38.

TABLE 8 Summary Results for SNP Swap Strain Engineering for Lysine Production Mean Lysine Yield (change in A₅₆₀ compared % % to reference Change over Change SNP N strain) Std Error Reference error DSS_033 4 0.1062 0.00888 11.54348 2.895652 DSS_311 2 0.03603 0.01256 3.916304 4.095652 DSS_350 1 0.03178 0.01777 3.454348 5.794565 DSS_056 3 0.02684 0.01026 2.917391 3.345652 DSS_014 4 0.02666 0.00888 2.897826 2.895652 DSS_338 3 0.02631 0.01026 2.859783 3.345652 DSS_128 1 0.02584 0.01777 2.808696 5.794565 DSS_038 4 0.02467 0.00888 2.681522 2.895652 DSS_066 4 0.02276 0.00888 2.473913 2.895652 DSS_108 2 0.02216 0.01256 2.408696 4.095652 DSS_078 4 0.02169 0.00888 2.357609 2.895652 DSS_017 3 0.02102 0.01026 2.284783 3.345652 DSS_120 3 0.01996 0.01026 2.169565 3.345652 DSS_064 4 0.01889 0.00888 2.053261 2.895652 DSS_380 4 0.01888 0.00888 2.052174 2.895652 DSS_105 3 0.0184 0.01026 2 3.345652 DSS_407 1 0.01831 0.01777 1.990217 5.794565 DSS_018 2 0.01825 0.01256 1.983696 4.095652 DSS_408 3 0.01792 0.01026 1.947826 3.345652 DSS_417 3 0.01725 0.01026 1.875 3.345652 DSS_130 3 0.01724 0.01026 1.873913 3.345652 DSS_113 4 0.0172 0.00888 1.869565 2.895652 DSS_355 3 0.01713 0.01026 1.861957 3.345652 DSS_121 3 0.01635 0.01026 1.777174 3.345652 DSS_097 2 0.0162 0.01256 1.76087 4.095652 DSS_107 3 0.01604 0.01026 1.743478 3.345652 DSS_110 2 0.01524 0.01256 1.656522 4.095652 DSS_306 4 0.01501 0.00888 1.631522 2.895652 DSS_316 1 0.01469 0.01777 1.596739 5.794565 DSS_325 4 0.01436 0.00888 1.56087 2.895652 DSS_016 4 0.01416 0.00888 1.53913 2.895652 DSS_324 4 0.01402 0.00888 1.523913 2.895652 DSS_297 4 0.01391 0.00888 1.511957 2.895652 DSS_118 2 0.01371 0.01256 1.490217 4.095652 DSS_100 2 0.01326 0.01256 1.441304 4.095652 DSS_019 1 0.01277 0.01777 1.388043 5.794565 DSS_131 3 0.01269 0.01026 1.379348 3.345652 DSS_394 4 0.01219 0.00888 1.325 2.895652 DSS_385 3 0.01192 0.01026 1.295652 3.345652 DSS_395 1 0.01162 0.01777 1.263043 5.794565 DSS_287 4 0.01117 0.00888 1.21413 2.895652 DSS_418 2 0.01087 0.01256 1.181522 4.095652 DSS_290 3 0.01059 0.01026 1.151087 3.345652 DSS_314 2 0.01036 0.01256 1.126087 4.095652 DSS_073 4 0.00986 0.00888 1.071739 2.895652 DSS_040 4 0.00979 0.00888 1.06413 2.895652 DSS_037 4 0.00977 0.00888 1.061957 2.895652 DSS_341 1 0.00977 0.01777 1.061957 5.794565 DSS_302 4 0.00939 0.00888 1.020652 2.895652 DSS_104 4 0.00937 0.00888 1.018478 2.895652 DSS_273 2 0.00915 0.01256 0.994565 4.095652 DSS_322 4 0.00906 0.00888 0.984783 2.895652 DSS_271 3 0.00901 0.01026 0.979348 3.345652 DSS_334 2 0.00898 0.01256 0.976087 4.095652 DSS_353 4 0.00864 0.00888 0.93913 2.895652 DSS_391 4 0.00764 0.00888 0.830435 2.895652 DSS_372 1 0.00737 0.01777 0.801087 5.794565 DSS_007 1 0.00729 0.01777 0.792391 5.794565 DSS_333 2 0.0072 0.01256 0.782609 4.095652 DSS_402 4 0.00718 0.00888 0.780435 2.895652 DSS_084 1 0.0069 0.01777 0.75 5.794565 DSS_103 3 0.00676 0.01026 0.734783 3.345652 DSS_362 1 0.00635 0.01777 0.690217 5.794565 DSS_012 2 0.00595 0.01256 0.646739 4.095652 DSS_396 2 0.00574 0.01256 0.623913 4.095652 DSS_133 3 0.00534 0.01026 0.580435 3.345652 DSS_065 3 0.00485 0.01026 0.527174 3.345652 DSS_284 2 0.00478 0.01256 0.519565 4.095652 DSS_301 3 0.00465 0.01026 0.505435 3.345652 DSS_281 4 0.00461 0.00888 0.501087 2.895652 DSS_405 2 0.00449 0.01256 0.488043 4.095652 DSS_361 3 0.00438 0.01026 0.476087 3.345652 DSS_342 4 0.00434 0.00888 0.471739 2.895652 DSS_053 3 0.00422 0.01026 0.458696 3.345652 DSS_074 4 0.00422 0.00888 0.458696 2.895652 DSS_079 4 0.00375 0.00888 0.407609 2.895652 DSS_381 3 0.0036 0.01026 0.391304 3.345652 DSS_294 1 0.00336 0.01777 0.365217 5.794565 DSS_313 2 0.00332 0.01256 0.36087 4.095652 DSS_388 2 0.00305 0.01256 0.331522 4.095652 DSS_392 4 0.00287 0.00888 0.311957 2.895652 DSS_319 4 0.00282 0.00888 0.306522 2.895652 DSS_310 4 0.00263 0.00888 0.28587 2.895652 DSS_344 3 0.00259 0.01026 0.281522 3.345652 DSS_025 4 0.00219 0.00888 0.238043 2.895652 DSS_412 1 0.00204 0.01777 0.221739 5.794565 DSS_300 3 0.00188 0.01026 0.204348 3.345652 DSS_299 2 0.00185 0.01256 0.201087 4.095652 DSS_343 4 0.00184 0.00888 0.2 2.895652 DSS_330 3 0.00153 0.01026 0.166304 3.345652 DSS_416 4 0.00128 0.00888 0.13913 2.895652 DSS_034 3 0.00128 0.01026 0.13913 3.345652 DSS_291 2 0.00102 0.01256 0.11087 4.095652 DSS_115 4 0.00063 0.00888 0.068478 2.895652 DSS_288 4 0.00044 0.00888 0.047826 2.895652 DSS_309 4 0.00008 0.00888 0.008696 2.895652 DSS_125 3 0 0.01026 0 3.345652 DSS_358 3 −0.00015 0.01026 −0.0163 3.345652 DSS_099 2 −0.00015 0.01256 −0.0163 4.095652 DSS_111 4 −0.00017 0.00888 −0.01848 2.895652 DSS_359 3 −0.00022 0.01026 −0.02391 3.345652 DSS_015 4 −0.00043 0.00888 −0.04674 2.895652 DSS_060 3 −0.0007 0.01026 −0.07609 3.345652 DSS_098 2 −0.00088 0.01256 −0.09565 4.095652 DSS_379 4 −0.00089 0.00888 −0.09674 2.895652 DSS_356 4 −0.0009 0.00888 −0.09783 2.895652 DSS_278 4 −0.00095 0.00888 −0.10326 2.895652 DSS_368 4 −0.001 0.00888 −0.1087 2.895652 DSS_351 1 −0.0015 0.01777 −0.16304 5.794565 DSS_296 1 −0.0015 0.01777 −0.16304 5.794565 DSS_119 3 −0.00156 0.01026 −0.16957 3.345652 DSS_307 3 −0.00163 0.01026 −0.17717 3.345652 DSS_077 4 −0.00167 0.00888 −0.18152 2.895652 DSS_030 3 −0.00188 0.01026 −0.20435 3.345652 DSS_370 2 −0.00189 0.01256 −0.20543 4.095652 DSS_375 2 −0.00212 0.01256 −0.23043 4.095652 DSS_280 3 −0.00215 0.01026 −0.2337 3.345652 DSS_345 4 −0.00225 0.00888 −0.24457 2.895652 DSS_419 1 −0.00234 0.01777 −0.25435 5.794565 DSS_298 2 −0.00249 0.01256 −0.27065 4.095652 DSS_367 3 −0.0026 0.01026 −0.28261 3.345652 DSS_072 3 −0.00268 0.01026 −0.2913 3.345652 DSS_366 4 −0.00272 0.00888 −0.29565 2.895652 DSS_063 4 −0.00283 0.00888 −0.30761 2.895652 DSS_092 3 −0.00292 0.01026 −0.31739 3.345652 DSS_347 4 −0.0033 0.00888 −0.3587 2.895652 DSS_114 4 −0.0034 0.00888 −0.36957 2.895652 DSS_303 3 −0.00396 0.01026 −0.43043 3.345652 DSS_276 4 −0.00418 0.00888 −0.45435 2.895652 DSS_083 1 −0.00446 0.01777 −0.48478 5.794565 DSS_031 2 −0.00456 0.01256 −0.49565 4.095652 DSS_328 3 −0.00463 0.01026 −0.50326 3.345652 DSS_039 4 −0.00475 0.00888 −0.5163 2.895652 DSS_331 4 −0.00475 0.00888 −0.5163 2.895652 DSS_117 4 −0.00485 0.00888 −0.52717 2.895652 DSS_382 4 −0.00506 0.00888 −0.55 2.895652 DSS_323 4 −0.00507 0.00888 −0.55109 2.895652 DSS_041 2 −0.00527 0.01256 −0.57283 4.095652 DSS_069 4 −0.00534 0.00888 −0.58043 2.895652 DSS_308 3 −0.00534 0.01026 −0.58043 3.345652 DSS_365 3 −0.00536 0.01026 −0.58261 3.345652 DSS_403 3 −0.00594 0.01026 −0.64565 3.345652 DSS_376 1 −0.00648 0.01777 −0.70435 5.794565 DSS_293 3 −0.00652 0.01026 −0.7087 3.345652 DSS_286 1 −0.00672 0.01777 −0.73043 5.794565 BS.2C 139 −0.00694 0.00151 −0.75435 0.492391 DSS_410 1 −0.00724 0.01777 −0.78696 5.794565 DSS_312 2 −0.00725 0.01256 −0.78804 4.095652 DSS_336 1 −0.00747 0.01777 −0.81196 5.794565 DSS_327 2 −0.00748 0.01256 −0.81304 4.095652 DSS_127 4 −0.00801 0.00888 −0.87065 2.895652 DSS_332 3 −0.0085 0.01026 −0.92391 3.345652 DSS_054 2 −0.00887 0.01256 −0.96413 4.095652 DSS_024 2 −0.00902 0.01256 −0.98043 4.095652 DSS_106 3 −0.0096 0.01026 −1.04348 3.345652 DSS_400 4 −0.00964 0.00888 −1.04783 2.895652 DSS_346 3 −0.00976 0.01026 −1.06087 3.345652 DSS_320 1 −0.01063 0.01777 −1.15543 5.794565 DSS_275 4 −0.01066 0.00888 −1.1587 2.895652 DSS_371 3 −0.01111 0.01026 −1.20761 3.345652 DSS_277 1 −0.01315 0.01777 −1.42935 5.794565 DSS_282 3 −0.01326 0.01026 −1.4413 3.345652 DSS_393 3 −0.01379 0.01026 −1.49891 3.345652 DSS_378 3 −0.01461 0.01026 −1.58804 3.345652 DSS_289 3 −0.01563 0.01026 −1.69891 3.345652 DSS_317 1 −0.01565 0.01777 −1.70109 5.794565 DSS_062 4 −0.01626 0.00888 −1.76739 2.895652 DSS_340 1 −0.01657 0.01777 −1.80109 5.794565 DSS_109 2 −0.01706 0.01256 −1.85435 4.095652 DSS_011 2 −0.0178 0.01256 −1.93478 4.095652 DSS_089 4 −0.01844 0.00888 −2.00435 2.895652 DSS_059 1 −0.01848 0.01777 −2.0087 5.794565 DSS_112 2 −0.01959 0.01256 −2.12935 4.095652 DSS_043 2 −0.0213 0.01256 −2.31522 4.095652 DSS_413 1 −0.02217 0.01777 −2.40978 5.794565 DSS_305 4 −0.0227 0.00888 −2.46739 2.895652 DSS_045 4 −0.02289 0.00888 −2.48804 2.895652 DSS_082 2 −0.0231 0.01256 −2.51087 4.095652 DSS_272 1 −0.02311 0.01777 −2.51196 5.794565 DSS_390 4 −0.02319 0.00888 −2.52065 2.895652 DSS_010 3 −0.02424 0.01026 −2.63478 3.345652 DSS_357 2 −0.02525 0.01256 −2.74457 4.095652 DSS_085 4 −0.03062 0.00888 −3.32826 2.895652 DSS_044 3 −0.04088 0.01026 −4.44348 3.345652 DSS_315 2 −0.0501 0.01256 −5.44565 4.095652 DSS_080 2 −0.13519 0.01256 −14.6946 4.095652 B. Second Round HTP Engineering and High Throughput Screening-Consolidation of SNP Swap Library with Selected PRO Swap Hits

One of the strengths of the HTP methods of the present disclosure is their ability to store HTP genetic design libraries together with information associated with each SNP/Promoter/Terminator/Start Codon's effects on host cell phenotypes. The present inventors had previously conducted a promoter swap experiment that had identified several zwf promoter swaps in C. glutamicum with positive effects on biosynthetic yields (see e.g., results for target “N” in FIG. 22).

The present inventors modified the base strain A of this Example to also include one of the previously identified zwf promoter swaps from Example 5. The top 176 SNPs identified from the initial screen described above in Table 8 were re-introduced into this new base strain to create a new SNP swap genetic design microbial library. As with the previous step, each newly created strain comprising a single SNP was tested for lysine yield. Selected SNP mutant strains were also tested for a productivity proxy, by measuring lysine production at 24 hours using the colorimetric method described supra. The results from this step are summarized in Table 9 below, and are depicted in FIG. 39.

TABLE 9 Second Round Screening for SNP Swap Strain Engineering for Lysine Production Mean Mean N for N for 24 hr 96 hr Std Error Std Error Strain ID SNP 24 hr 96 hr (A₅₆₀) (A₅₆₀) 24 hr 96 hr 7000006318 BS2C_P0007_39zwf 20 2 0.49 0.82 0.00 0.02 7000008538 DSS_002 4 2 0.53 0.78 0.01 0.02 7000008539 DSS_003 4 0.56 0.01 7000008541 DSS_005 4 0.27 0.01 7000008542 DSS_006 4 0.49 0.01 7000008547 DSS_011 4 0.55 0.01 7000008548 DSS_012 4 0.58 0.01 7000008549 DSS_013 4 0.56 0.01 7000008550 DSS_014 4 0.52 0.01 7000008551 DSS_015 4 0.54 0.01 7000008552 DSS_016 4 2 0.50 0.84 0.01 0.02 7000008553 DSS_017 4 0.44 0.01 7000008555 DSS_019 4 4 0.46 0.84 0.01 0.01 7000008557 DSS_021 4 4 0.46 0.86 0.01 0.01 7000008559 DSS_023 4 2 0.55 0.86 0.01 0.02 7000008561 DSS_025 4 0.54 0.01 7000008562 DSS_026 2 0.46 0.01 7000008564 DSS_028 4 0.51 0.01 7000008565 DSS_029 4 4 0.48 0.87 0.01 0.01 7000008566 DSS_030 4 4 0.47 0.85 0.01 0.01 7000008567 DSS_031 4 0.56 0.01 7000008569 DSS_033 4 4 0.46 0.86 0.01 0.01 7000008570 DSS_034 2 2 0.53 0.85 0.01 0.02 7000008573 DSS_037 4 0.54 0.01 7000008574 DSS_038 4 0.53 0.01 7000008575 DSS_039 4 0.55 0.01 7000008576 DSS_040 4 0.57 0.01 7000008577 DSS_041 4 0.45 0.01 7000008578 DSS_042 4 4 0.52 0.87 0.01 0.01 7000008579 DSS_043 4 4 0.45 0.87 0.01 0.01 7000008580 DSS_044 4 2 0.50 0.85 0.01 0.02 7000008581 DSS_045 4 0.47 0.01 7000008582 DSS_046 4 2 0.61 0.85 0.01 0.02 7000008583 DSS_047 4 2 0.61 0.82 0.01 0.02 7000008586 DSS_050 4 0.57 0.01 7000008587 DSS_051 4 0.56 0.01 7000008588 DSS_052 4 2 0.49 0.85 0.01 0.02 7000008589 DSS_053 4 4 0.45 0.85 0.01 0.01 7000008590 DSS_054 4 4 0.45 0.88 0.01 0.01 7000008592 DSS_056 4 0.42 0.01 7000008596 DSS_060 4 2 0.55 0.87 0.01 0.02 7000008597 DSS_061 4 2 0.37 0.86 0.01 0.02 7000008598 DSS_062 4 4 0.45 0.87 0.01 0.01 7000008601 DSS_065 4 4 0.47 0.88 0.01 0.01 7000008602 DSS_066 4 0.47 0.01 7000008604 DSS_068 2 0.51 0.02 7000008605 DSS_069 4 4 0.47 0.88 0.01 0.01 7000008606 DSS_070 4 0.55 0.01 7000008607 DSS_071 4 2 0.56 0.84 0.01 0.02 7000008608 DSS_072 4 2 0.54 0.83 0.01 0.02 7000008609 DSS_073 4 2 0.47 0.84 0.01 0.02 7000008610 DSS_074 4 2 0.51 0.83 0.01 0.02 7000008612 DSS_076 4 4 0.48 0.76 0.01 0.01 7000008613 DSS_077 4 4 0.46 0.87 0.01 0.01 7000008614 DSS_078 4 2 0.44 0.87 0.01 0.02 7000008615 DSS_079 4 2 0.47 0.90 0.01 0.02 7000008616 DSS_080 4 2 0.48 0.81 0.01 0.02 7000008619 DSS_083 4 2 0.59 0.86 0.01 0.02 7000008620 DSS_084 4 2 0.70 0.89 0.01 0.02 7000008621 DSS_085 4 4 0.49 0.89 0.01 0.01 7000008622 DSS_086 4 2 0.48 0.82 0.01 0.02 7000008624 DSS_088 4 2 0.47 0.88 0.01 0.02 7000008625 DSS_089 4 4 0.45 0.89 0.01 0.01 7000008626 DSS_090 4 4 0.47 0.87 0.01 0.01 7000008627 DSS_091 4 0.46 0.01 7000008629 DSS_093 4 4 0.50 0.87 0.01 0.01 7000008630 DSS_094 4 2 0.57 0.86 0.01 0.02 7000008634 DSS_098 4 2 0.53 0.85 0.01 0.02 7000008636 DSS_100 4 0.52 0.01 7000008637 DSS_101 4 2 0.49 0.85 0.01 0.02 7000008640 DSS_104 4 2 0.51 0.84 0.01 0.02 7000008645 DSS_109 4 0.51 0.01 7000008646 DSS_110 4 2 0.57 0.86 0.01 0.02 7000008648 DSS_112 4 2 0.54 0.86 0.01 0.02 7000008651 DSS_115 4 0.49 0.01 7000008652 DSS_116 4 2 0.52 0.82 0.01 0.02 7000008653 DSS_117 4 2 0.50 0.84 0.01 0.02 7000008657 DSS_121 4 2 0.78 0.88 0.01 0.02 7000008659 DSS_123 4 0.54 0.01 7000008663 DSS_127 4 0.58 0.01 7000008665 DSS_129 4 0.48 0.01 7000008666 DSS_130 4 0.56 0.01 7000008669 DSS_133 4 0.50 0.01 7000008670 DSS_271 4 2 0.52 0.86 0.01 0.02 7000008672 DSS_273 4 0.56 0.01 7000008677 DSS_278 2 0.46 0.01 7000008678 DSS_279 4 0.55 0.01 7000008681 DSS_282 4 0.51 0.01 7000008683 DSS_284 4 0.59 0.01 7000008684 DSS_285 4 0.51 0.01 7000008685 DSS_286 4 0.56 0.01 7000008687 DSS_288 4 0.46 0.01 7000008688 DSS_289 4 0.57 0.01 7000008689 DSS_290 4 0.47 0.01 7000008693 DSS_294 4 2 0.52 0.63 0.01 0.02 7000008696 DSS_297 4 2 0.52 0.86 0.01 0.02 7000008697 DSS_298 4 0.58 0.01 7000008699 DSS_300 4 0.48 0.01 7000008700 DSS_301 4 0.58 0.01 7000008701 DSS_302 4 0.47 0.01 7000008702 DSS_303 3 0.46 0.01 7000008703 DSS_304 3 0.48 0.01 7000008705 DSS_306 4 2 0.53 0.80 0.01 0.02 7000008708 DSS_309 4 0.56 0.01 7000008709 DSS_310 4 0.56 0.01 7000008711 DSS_312 4 0.55 0.01 7000008712 DSS_313 4 0.51 0.01 7000008718 DSS_319 4 2 0.50 0.82 0.01 0.02 7000008720 DSS_321 4 0.56 0.01 7000008722 DSS_323 2 2 0.48 0.85 0.01 0.02 7000008723 DSS_324 4 0.55 0.01 7000008724 DSS_325 4 0.50 0.01 7000008725 DSS_326 3 0.46 0.01 7000008726 DSS_327 3 0.47 0.01 7000008730 DSS_331 4 0.56 0.01 7000008731 DSS_332 4 4 0.47 0.89 0.01 0.01 7000008732 DSS_333 4 4 0.47 0.87 0.01 0.01 7000008733 DSS_334 4 0.45 0.01 7000008734 DSS_335 2 0.47 0.01 7000008735 DSS_336 4 0.47 0.01 7000008739 DSS_340 4 0.46 0.01 7000008740 DSS_341 4 2 0.46 0.89 0.01 0.02 7000008741 DSS_342 4 0.56 0.01 7000008742 DSS_343 4 0.55 0.01 7000008743 DSS_344 4 4 0.48 0.87 0.01 0.01 7000008746 DSS_347 4 4 0.48 0.85 0.01 0.01 7000008747 DSS_348 4 4 0.46 0.86 0.01 0.01 7000008749 DSS_350 4 2 0.29 0.74 0.01 0.02 7000008752 DSS_353 4 2 0.46 0.85 0.01 0.02 7000008753 DSS_354 4 4 0.45 0.87 0.01 0.01 7000008755 DSS_356 4 4 0.46 0.86 0.01 0.01 7000008756 DSS_357 4 4 0.46 0.86 0.01 0.01 7000008758 DSS_359 2 2 0.45 0.85 0.01 0.02 7000008760 DSS_361 4 2 0.46 0.84 0.01 0.02 7000008761 DSS_362 4 0.44 0.01 7000008763 DSS_364 4 0.44 0.01 7000008764 DSS_365 4 0.46 0.01 7000008765 DSS_366 4 0.55 0.01 7000008766 DSS_367 4 0.55 0.01 7000008767 DSS_368 4 2 0.44 0.86 0.01 0.02 7000008770 DSS_371 4 2 0.47 0.88 0.01 0.02 7000008771 DSS_372 4 2 0.46 0.83 0.01 0.02 7000008772 DSS_373 4 2 0.46 0.88 0.01 0.02 7000008774 DSS_375 4 0.45 0.01 7000008776 DSS_377 4 0.45 0.01 7000008777 DSS_378 4 0.57 0.01 7000008778 DSS_379 4 0.54 0.01 7000008779 DSS_380 4 2 0.46 0.87 0.01 0.02 7000008781 DSS_382 4 2 0.46 0.84 0.01 0.02 7000008782 DSS_383 4 0.48 0.01 7000008783 DSS_384 4 2 0.47 0.82 0.01 0.02 7000008784 DSS_385 4 2 0.46 0.83 0.01 0.02 7000008786 DSS_387 3 0.43 0.01 7000008787 DSS_388 3 0.47 0.01 7000008788 DSS_389 4 2 0.46 0.89 0.01 0.02 7000008790 DSS_391 4 0.57 0.01 7000008791 DSS_392 4 0.44 0.01 7000008795 DSS_396 4 2 0.46 0.82 0.01 0.02 7000008799 DSS_400 4 0.47 0.01 7000008800 DSS_401 4 2 0.46 0.86 0.01 0.02 7000008801 DSS_402 4 0.54 0.01 7000008805 DSS_406 4 2 0.47 0.85 0.01 0.02 7000008807 DSS_408 4 0.45 0.01 7000008810 DSS_411 4 2 0.46 0.87 0.01 0.02 7000008812 DSS_413 3 0.47 0.01 7000008813 DSS_414 4 2 0.45 0.84 0.01 0.02 7000008815 DSS_416 4 2 0.45 0.87 0.01 0.02 7000008816 DSS_417 4 0.46 0.01 7000008818 DSS_419 4 2 0.47 0.84 0.01 0.02 7000008820 DSS_421 4 2 0.45 0.79 0.01 0.02 7000008821 DSS_422 4 0.44 0.01

The results from this second round of SNP swap identified several SNPs capable of increasing base strain yield and productivity of lysine in a base strain comprising the zwf promoter swap mutation (see e.g., SNP 084 and SNP 121 on the upper right hand corner of FIG. 39).

C. Tank Culture Validation

Strains containing top SNPs identified during the HTP steps above were cultured into medium sized test fermentation tanks. Briefly, small 100 ml cultures of each strain were grown over night, and were then used to inoculate 5 liter cultures in the test fermentation tanks with equal amounts of inoculate. The inoculate was normalized to contain the same cellular density following an OD600 measurement.

The resulting tank cultures were allowed to proceed for 3 days before harvest. Yield and productivity measurements were calculated from substrate and product titers in samples taken from the tank at various points throughout the fermentation. Samples were analyzed for particular small molecule concentrations by high pressure liquid chromatography using the appropriate standards. Results for this experiment are summarized in Table 10 below, and depicted in FIG. 40.

TABLE 10 Tank Validation of SNP Swap Microbes Mean Yield (%) (g lysine produced/g Mean glucose Std Productivity Std Strain N consumed) Error (g/L/h) Error base strain 1 41.1502 0.59401 3.29377 0.24508 base strain + zwf 7 48.2952 0.22451 2.73474 0.10005 base strain + zwf + 2 50.325 0.42003 4.51397 0.1733 SNP121 base strain + zwf + 5 52.191 0.26565 4.15269 0.12254 pyc + lysA

As predicted by the small scale high throughput cultures, larger tank cultures for strains comprising the combined zwf promoter swap and SNP 121 exhibited significant increases in yield and productivity over the base reference strain. Productivity of this strain for example, jumped to 4.5 g/L/h compared to the 3.29 g/L/h productivity of the base strain (a 37.0% increase in productivity in only 2 rounds of SNP Swap).

Example 4: HTP Genomic Engineering—Implementation of a Promoter Swap Library to Improve an Industrial Microbial Strain

Previous examples have demonstrated the power of the HTP strain improvement programs of the present disclosure for rehabilitating industrial strains. Examples 2 and 3 described the implementation of SNP swap techniques and libraries exploring the existing genetic diversity within various base, intermediate, and industrial strains

This example illustrates embodiments of the HTP strain improvement programs using the PRO swap techniques of the present disclosure. Unlike Example 3, this example teaches methods for the de-novo generation of mutations via PRO swap library generation.

A. Identification of a Target for Promoter Swapping

As aforementioned, promoter swapping is a multi-step process that comprises a step of: Selecting a set of “n” genes to target.

In this example, the inventors have identified a group of 23 potential pathway genes to modulate via the promoter ladder methods of the present disclosure (19 genes to overexpress and 4+ diverting genes to downregulate, in an exemplary metabolic pathway producing the molecule lysine). (See, FIG. 19).

B. Creation of Promoter Ladder

Another step in the implementation of a promoter swap process is the selection of a set of “x” promoters to act as a “ladder”. Ideally these promoters have been shown to lead to highly variable expression across multiple genomic loci, but the only requirement is that they perturb gene expression in some way.

These promoter ladders, in particular embodiments, are created by: identifying natural, native, or wild-type promoters associated with the target gene of interest and then mutating said promoter to derive multiple mutated promoter sequences. Each of these mutated promoters is tested for effect on target gene expression. In some embodiments, the edited promoters are tested for expression activity across a variety of conditions, such that each promoter variant's activity is documented/characterized/annotated and stored in a database. The resulting edited promoter variants are subsequently organized into “ladders” arranged based on the strength of their expression (e.g., with highly expressing variants near the top, and attenuated expression near the bottom, therefore leading to the term “ladder”).

In the present exemplary embodiment, the inventors have created promoter ladder:ORF combinations for each of the target genes identified in FIG. 19.

C. Associating Promoters from the Ladder with Target Genes

Another step in the implementation of a promoter swap process is the HTP engineering of various strains that comprise a given promoter from the promoter ladder associated with a particular target gene.

If a native promoter exists in front of target gene n and its sequence is known, then replacement of the native promoter with each of the x promoters in the ladder can be carried out. When the native promoter does not exist or its sequence is unknown, then insertion of each of the x promoters in the ladder in front of gene n can be carried out. In this way a library of strains is constructed, wherein each member of the library is an instance of x promoter operably linked to n target, in an otherwise identical genetic context (see e.g., FIG. 20).

D. HTP Screening of the Strains

A final step in the promoter swap process is the HTP screening of the strains in the aforementioned library. Each of the derived strains represents an instance of x promoter linked to n target, in an otherwise identical genetic background.

By implementing a HTP screening of each strain, in a scenario where their performance against one or more metrics is characterized, the inventors are able to determine what promoter/target gene association is most beneficial for a given metric (e.g. optimization of production of a molecule of interest). See, FIG. 20 (promoters P1-P8 effect on gene of interest).

In the exemplary embodiment illustrated in FIGS. 19-22, the inventors have utilized the promoter swap process to optimize the production of lysine. An application of the Pro SWAP methods described above is described in Example 5, below.

Example 5: HTP Genomic Engineering—Implementation of a PRO Swap Library to Improve Strain Performance for Lysine Production

The section below provides an illustrative implementation of the PRO swap HTP design strain improvement program tools of the present disclosure, as described in Example 4. In this example, a Corynebacterium strain was subjected to the PRO swap methods of the present disclosure in order to increase host cell yield of lysine.

A. Promoter Swap

Promoter Swaps were conducted as described in Example 4. Selected genes from the Lysine biosynthetic pathway in FIG. 19 were targeted for promoter swaps using promoters P1-P8.

B. HTP Engineering and High Throughput Screening

HTP engineering of the promoter swaps was conducted as described in Example 1 and 3. HTP screening of the resulting promoter swap strains was conducted as described in Example 3. In total 145 PRO swaps were conducted. The results of the experiment are summarized in Table 11 below, and are depicted in FIG. 41.

TABLE 11 HTP Screening of Lysine PRO Swap Libraries Mean % Yield Change From Strain promoter-target N (A₅₆₀) Std Error Base 7000007713 Pcg1860-asd 8 0.84595 0.00689 3.927615 7000007736 Pcg0755-asd 4 0.84036 0.00974 3.240866 7000007805 Pcg0007_119-asd 8 0.82493 0.00689 1.345242 7000007828 Pcg3121-asd 8 0.8246 0.00689 1.3047 7000007759 Pcg0007_265-asd 8 0.81155 0.00689 −0.29853 7000007782 Pcg3381-asd 8 0.8102 0.00689 −0.46438 7000007712 Pcg1860-ask 8 0.83958 0.00689 3.14504 7000007735 Pcg0755-ask 8 0.81673 0.00689 0.337846 7000007827 Pcg3121-ask 8 0.81498 0.00689 0.122853 7000007804 Pcg0007_119-ask 8 0.81492 0.00689 0.115482 7000007758 Pcg0007_265-ask 8 0.80381 0.00689 −1.24942 7000007781 Pcg3381-ask 8 0.80343 0.00689 −1.2961 7000007780 Pcg3381-aspB 8 0.84072 0.00689 3.285093 7000007803 Pcg0007_119- 8 0.82106 0.00689 0.8698 aspB 7000007809 Pcg0007_119- 8 0.83446 0.00689 2.516032 cg0931 7000007717 Pcg1860-cg0931 4 0.83129 0.00974 2.126588 7000007763 Pcg0007_265- 4 0.82628 0.00974 1.511094 cg0931 7000007671 Pcg0007_39- 8 0.82554 0.00689 1.420182 cg0931 7000007740 Pcg0755-cg0931 8 0.81921 0.00689 0.642522 7000007694 Pcg0007-cg0931 8 0.80444 0.00689 −1.17202 7000007691 Pcg0007-dapA 8 0.8299 0.00689 1.955822 7000007783 Pcg3381-dapA 8 0.80951 0.00689 −0.54915 7000007760 Pcg0007_265- 8 0.76147 0.00689 −6.45102 dapA 7000007806 Pcg0007_119- 8 0.35394 0.00689 −56.5174 dapA 7000007761 Pcg0007_265- 8 0.84157 0.00689 3.389518 dapB 7000007738 Pcg0755-dapB 4 0.84082 0.00974 3.297378 7000007692 Pcg0007-dapB 8 0.83088 0.00689 2.076218 7000007784 Pcg3381-dapB 8 0.82474 0.00689 1.3219 7000007715 Pcg1860-dapB 8 0.82232 0.00689 1.024595 7000007830 Pcg3121-dapB 8 0.81236 0.00689 −0.19902 7000007807 Pcg0007_119- 4 0.69622 0.00974 −14.4672 dapB 7000007762 Pcg0007_265- 8 0.84468 0.00689 3.771591 dapD 7000007808 Pcg0007_119- 8 0.83869 0.00689 3.035701 dapD 7000007785 Pcg3381-dapD 8 0.83397 0.00689 2.455834 7000007670 Pcg0007_39- 8 0.81698 0.00689 0.368559 dapD 7000007831 Pcg3121-dapD 4 0.8155 0.00974 0.186737 7000007693 Pcg0007-dapD 8 0.8117 0.00689 −0.28011 7000007716 Pcg1860-dapD 8 0.79044 0.00689 −2.89196 7000007739 Pcg0755-dapD 8 0.78694 0.00689 −3.32195 7000007787 Pcg3381-dapE 8 0.83814 0.00689 2.968132 7000007833 Pcg3121-dapE 8 0.83721 0.00689 2.853878 7000007741 Pcg0755-dapE 8 0.83263 0.00689 2.291211 7000007810 Pcg0007_119- 8 0.83169 0.00689 2.175729 dapE 7000007718 Pcg1860-dapE 8 0.81855 0.00689 0.561439 7000007672 Pcg0007_39-dapE 8 0.80932 0.00689 −0.5725 7000007765 Pcg0007_265- 8 0.8327 0.00689 2.299811 dapF 7000007788 Pcg3381-dapF 8 0.82942 0.00689 1.896853 7000007811 Pcg0007_119- 8 0.82926 0.00689 1.877196 dapF 7000007696 Pcg0007-dapF 8 0.82099 0.00689 0.861201 7000007719 Pcg1860-dapF 8 0.82067 0.00689 0.821888 7000007673 Pcg0007_39-dapF 8 0.82062 0.00689 0.815745 7000007789 Pcg3381-ddh 8 0.84817 0.00689 4.200349 7000007835 Pcg3121-ddh 8 0.82141 0.00689 0.912799 7000007812 Pcg0007_119-ddh 8 0.82093 0.00689 0.853829 7000007674 Pcg0007_39-ddh 8 0.81494 0.00689 0.117939 7000007720 Pcg1860-ddh 8 0.81473 0.00689 0.09214 7000007766 Pcg0007_265-ddh 8 0.81427 0.00689 0.035627 7000007743 Pcg0755-ddh 8 0.80655 0.00689 −0.9128 7000007697 Pcg0007-ddh 8 0.80621 0.00689 −0.95457 7000007779 Pcg3381-fbp 8 0.85321 0.00689 4.819529 7000007802 Pcg0007_119-fbp 4 0.81425 0.00974 0.03317 7000007710 Pcg1860-fbp 4 0.40253 0.00974 −50.5479 7000007687 Pcg0007-fbp 8 0.14881 0.00689 −81.7182 7000007825 Pcg3121-fbp 4 0.12471 0.00974 −84.679 7000007733 Pcg0755-fbp 4 0.08217 0.00974 −89.9052 7000007746 Pcg0755-hom 8 0.81925 0.00689 0.647436 7000007792 Pcg3381-hom 4 0.77674 0.00974 −4.57505 7000007723 Pcg1860-hom 8 0.71034 0.00689 −12.7325 7000007838 Pcg3121-hom 8 0.559 0.00689 −31.3251 7000007800 Pcg0007_119-icd 8 0.83236 0.00689 2.258041 7000007823 Pcg3121-icd 8 0.83155 0.00689 2.15853 7000007777 Pcg3381-icd 8 0.82844 0.00689 1.776456 7000007708 Pcg1860-icd 8 0.82384 0.00689 1.211332 7000007662 Pcg0007_39-icd 12 0.82008 0.00562 0.749404 7000007685 Pcg0007-icd 8 0.81257 0.00689 −0.17322 7000007754 Pcg0007_265-icd 4 0.81172 0.00974 −0.27765 7000007698 Pcg0007-lysA 4 0.8504 0.00974 4.474311 7000007675 Pcg0007_39-lysA 8 0.84414 0.00689 3.705251 7000007836 Pcg3121-lysA 4 0.83545 0.00974 2.637657 7000007767 Pcg0007_265- 8 0.83249 0.00689 2.274012 lysA 7000007813 Pcg0007_119- 8 0.83096 0.00689 2.086046 lysA 7000007790 Pcg3381-lysA 8 0.8118 0.00689 −0.26782 7000007676 Pcg0007_39-lysE 8 0.84394 0.00689 3.68068 7000007699 Pcg0007-lysE 4 0.83393 0.00974 2.45092 7000007768 Pcg0007_265- 8 0.83338 0.00689 2.383351 lysE 7000007837 Pcg3121-lysE 4 0.83199 0.00974 2.212585 7000007791 Pcg3381-lysE 8 0.81476 0.00689 0.095825 7000007814 Pcg0007_119- 8 0.81315 0.00689 −0.10197 lysE 7000007775 Pcg3381-odx 8 0.82237 0.00689 1.030738 7000007752 Pcg0007_265-odx 8 0.81118 0.00689 −0.34399 7000007729 Pcg0755-odx 8 0.81103 0.00689 −0.36242 7000007683 Pcg0007-odx 8 0.80507 0.00689 −1.09462 7000007706 Pcg1860-odx 4 0.79332 0.00974 −2.53815 7000007660 Pcg0007_39-odx 8 0.79149 0.00689 −2.76297 7000007798 Pcg0007_119-odx 8 0.77075 0.00689 −5.31094 7000007821 Pcg3121-odx 4 0.74788 0.00974 −8.12059 7000007822 Pcg3121-pck 8 0.85544 0.00689 5.093491 7000007776 Pcg3381-pck 8 0.8419 0.00689 3.43006 7000007799 Pcg0007_119-pck 8 0.83851 0.00689 3.013588 7000007753 Pcg0007_265-pck 8 0.82738 0.00689 1.646232 7000007730 Pcg0755-pck 4 0.81785 0.00974 0.475442 7000007661 Pcg0007_39-pck 8 0.80976 0.00689 −0.51844 7000007684 Pcg0007-pck 8 0.79007 0.00689 −2.93742 7000007707 Pcg1860-pck 8 0.71566 0.00689 −12.0789 7000007840 Pcg3121-pgi 4 1.01046 0.00974 24.13819 7000007817 Pcg0007_119-pgi 7 0.99238 0.00736 21.917 7000007794 Pcg3381-pgi 7 0.99008 0.00736 21.63444 7000007771 Pcg0007_265-pgi 8 0.94665 0.00689 16.29893 7000007725 Pcg1860-pgi 8 0.85515 0.00689 5.057864 7000007702 Pcg0007-pgi 4 0.8056 0.00974 −1.02951 7000007658 Pcg0007_39-ppc 4 0.85221 0.00974 4.696676 7000007750 Pcg0007_265-ppc 8 0.84486 0.00689 3.793705 7000007727 Pcg0755-ppc 8 0.84166 0.00689 3.400575 7000007773 Pcg3381-ppc 4 0.82883 0.00974 1.824369 7000007796 Pcg0007_119-ppc 8 0.82433 0.00689 1.27153 7000007704 Pcg1860-ppc 8 0.81736 0.00689 0.415244 7000007819 Pcg3121-ppc 8 0.79898 0.00689 −1.8428 7000007732 Pcg0755-ptsG 8 0.84055 0.00689 3.264208 7000007709 Pcg1860-ptsG 8 0.81075 0.00689 −0.39682 7000007663 Pcg0007_39-ptsG 8 0.80065 0.00689 −1.63763 7000007778 Pcg3381-ptsG 8 0.23419 0.00689 −71.229 7000007801 Pcg0007_119- 8 0.17295 0.00689 −78.7525 ptsG 7000007824 Pcg3121-ptsG 8 0.16035 0.00689 −80.3005 7000007705 Pcg1860-pyc 8 0.85143 0.00689 4.60085 7000007728 Pcg0755-pyc 8 0.79803 0.00689 −1.95951 7000007659 Pcg0007_39-pyc 8 0.75539 0.00689 −7.19797 7000007751 Pcg0007_265-pyc 8 0.73664 0.00689 −9.50146 7000007682 Pcg0007-pyc 4 0.73142 0.00974 −10.1428 7000007774 Pcg3381-pyc 4 0.66667 0.00974 −18.0975 7000007797 Pcg0007_119-pyc 4 0.52498 0.00974 −35.5046 7000007820 Pcg3121-pyc 8 0.52235 0.00689 −35.8277 7000007841 Pcg3121-tkt 8 0.82565 0.00689 1.433696 7000007818 Pcg0007_119-tkt 8 0.81674 0.00689 0.339075 7000007749 Pcg0755-tkt 8 0.81496 0.00689 0.120396 7000007703 Pcg0007-tkt 4 0.76763 0.00974 −5.69424 7000007795 Pcg3381-tkt 8 0.72213 0.00689 −11.2841 7000007772 Pcg0007_265-tkt 8 0.68884 0.00689 −15.3738 7000007701 Pcg0007-zwf 4 0.95061 0.00974 16.78542 7000007747 Pcg0755-zwf 8 0.92595 0.00689 13.75587 7000007770 Pcg0007_265-zwf 8 0.9029 0.00689 10.9241 7000007724 Pcg1860-zwf 8 0.79309 0.00689 −2.5664 7000007839 Pcg3121-zwf 4 0.13379 0.00974 −83.5635 7000000017 — 116 0.92115 0.00181 13.16617 7000006284 — 128 0.81398 0.00172 0 7000005754 — 64 0.79489 0.00243 −2.34527

When visualized, the results of the promoter swap library screening serve to identify gene targets that are most closely correlated with the performance metric being measured. In this case, gene targets pgi, zwf, ppc, pck, fbp, and ddh were identified as genes for which promoter swaps produce large gains in yield over base strains.

Selected strains from Table 11 were re-cultured in small plates and tested for lysine yield as describe above. The results from this secondary screening are provided in FIG. 22.

Example 6: Epistasis Mapping—An Algorithmic Tool for Predicting Beneficial Mutation Consolidations

This example describes an embodiment of the predictive modeling techniques utilized as part of the HTP strain improvement program of the present disclosure. After an initial identification of potentially beneficial mutations (through the use of genetic design libraries as described above), the present disclosure teaches methods of consolidating beneficial mutations in second, third, fourth, and additional subsequent rounds of HTP strain improvement. In some embodiments, the present disclosure teaches that mutation consolidations may be based on the individual performance of each of said mutations. In other embodiments, the present disclosure teaches methods for predicting the likelihood that two or more mutations will exhibit additive or synergistic effects if consolidated into a single host cell. The example below illustrates an embodiment of the predicting tools of the present disclosure.

Selected mutations from the SNP swap and promoter swapping (PRO swap) libraries of Examples 3 and 5 were analyzed to identify SNP/PRO swap combinations that would be most likely to lead to strain host performance improvements.

SNP swapping library sequences were compared to each other using a cosine similarity matrix, as described in the “Epistasis Mapping” section of the present disclosure. The results of the analysis yielded functional similarity scores for each SNP/PRO swap combination. A visual representation of the functional similarities among all SNPs/PRO swaps is depicted in a heat map in FIG. 15. The resulting functional similarity scores were also used to develop a dendrogram depicting the similarity distance between each of the SNPs/PRO swaps (FIG. 16A).

Mutations from the same or similar functional group (i.e., SNPs/PRO swaps with high functional similarity) are more likely to operate by the same mechanism, and are thus more likely to exhibit negative or neutral epistasis on overall host performance when combined. In contrast, mutations from different functional groups would be more likely to operate by independent mechanisms, and thus more likely to produce beneficial additive or combinatorial effects on host performance.

In order to illustrate the effects of biological pathways on epistasis, SNPs and PRO swaps exhibiting various functional similarities were combined and tested on host strains. Three SNP/PRO swap combinations were engineered into the genome of Corynebacterium glutamicum as described in Example 1: 1) Pcg0007::zwf PRO swap+Pcg1860::pyc PRO swap, ii) Pcg0007::zwf PRO swap+SNP 309, and iv) Pcg0007::zwf PRO swap+Pcg0007::lysA PRO swap (see FIGS. 15 and 16A for functional similarity relationships).

The performance of each of the host cells containing the SNP/PRO swap combinations was tested as described in Example 3, and was compared to that of a control host cell containing only zwf PRO swap. Tables 12 and 13 below summarize the results of host cell yield (96 hr measurements) and productivity (24 hr measurements) of each of the strains.

TABLE 12 Lysine Accumulation for Epistasis Mapping Experiment at 24 hours. Mean Lysine SNP/PRO swap (A₅₆₀) StDev 6318 (zwf) 0.51 0.03 8126 (zwf + lysA) 0.88 0.06 8156 (zwf + pyc) 0.53 0.01 8708 (zwf + SNP 0.56 0.00 309)

TABLE 13 Lysine Accumulation for Epistasis Mapping Experiment at 96 hours. Mean Lysine SNP/PRO swap (A₅₆₀) StDev 6318 (zwf) 0.83 0.01 8126 (zwf + lysA) 0.94 0.02 8156 (zwf + pyc) 0.83 0.06

Host yield performance results for each SNP/PRO swap combination are also depicted in FIG. 16B. Host strains combining SNPs/PRO swaps exhibiting lower functional similarity outperformed strains in which the combined SNPs had exhibited higher functional similarity at both 24, and 96 hour measurements.

Thus, the epistatic mapping procedure is useful for predicting/programming/informing effective and/or positive consolidations of designed genetic changes. The analytical insight from the epistatic mapping procedure allows for the creation of predictive rule sets that can guide subsequent rounds of microbial strain development. The predictive insight gained from the epistatic library may be used across microbial types and target molecule types.

Example 7: HTP Genomic Engineering—Pro Swap Mutation Consolidation and Multi-Factor Combinatorial Testing

Previous examples have illustrated methods for consolidating a small number of pre-selected PRO swap mutations with SNP swap libraries (Example 3). Other examples have illustrated the epistatic methods for selecting mutation consolidations that are most likely to yield additive or synergistic beneficial host cell properties (Example 6). This example illustrates the ability of the HTP methods of the present disclosure to effectively explore the large solution space created by the combinatorial consolidation of multiple gene/genetic design library combinations (e.g., PRO swap library x SNP Library or combinations within a PRO swap library).

In this illustrative application of the HTP strain improvement methods of the present disclosure, promoter swaps identified as having a positive effect on host performance in Example 5 are consolidated in second order combinations with the original PRO swap library. The decision to consolidate PRO swap mutations was based on each mutation's overall effect on yield or productivity, and the likelihood that the combination of the two mutations would produce an additive or synergistic effect.

For example, applicants refer to their choice of combining Pcg0007::zwf and Pcg0007::lysA, based on the epistasis mapping results of Example 6.

A. Consolidation Round for PRO Swap Strain Engineering

Strains were transformed as described in previous Example 1. Briefly, strains already containing one desired PRO swap mutation were once again transformed with the second desired PRO swap mutation. In total, the 145 tested PRO swaps from Example 5 were consolidated into 53 second round consolidation strains, each comprising two PRO swap mutations expected to exhibit beneficial additive or synergistic effects.

The resulting second round strains were once again screened as described in Example 3. Results from this experiment are summarized in Table 14 below, and depicted in FIG. 11.

TABLE 14 HTP Screening of Second Round Consolidated Lysine PRO Swap Libraries Mean Strain ID Number PRO Swap 1 PRO Swap 2 Yield (A₅₆₀) Std Dev 7000008489 4 Pcg0007-lysA Pcg3121-pgi 1.17333 0.020121 7000008530 8 Pcg1860-pyc Pcg0007-zwf 1.13144 0.030023 7000008491 7 Pcg0007-lysA Pcg0007-zwf 1.09836 0.028609 7000008504 8 Pcg3121-pck Pcg0007-zwf 1.09832 0.021939 7000008517 8 Pcg0007_39- Pcg0007-zwf 1.09502 0.030777 ppc 7000008502 4 Pcg3121-pck Pcg3121-pgi 1.09366 0.075854 7000008478 4 Pcg3381-ddh Pcg0007-zwf 1.08893 0.025505 7000008465 4 Pcg0007_265- Pcg0007-zwf 1.08617 0.025231 dapB 7000008535 8 Pcg0007-zwf Pcg3121-pgi 1.06261 0.019757 7000008476 6 Pcg3381-ddh Pcg3121-pgi 1.04808 0.084307 7000008510 8 Pcg3121-pgi Pcg1860-pyc 1.04112 0.021087 7000008525 8 Pcg1860-pyc Pcg0007_265- 1.0319 0.034045 dapB 7000008527 8 Pcg1860-pyc Pcg0007-lysA 1.02278 0.043549 7000008452 5 Pcg1860-asd Pcg0007-zwf 1.02029 0.051663 7000008463 4 Pcg0007_265- Pcg3121-pgi 1.00511 0.031604 dapB 7000008524 8 Pcg1860-pyc Pcg1860-asd 1.00092 0.026355 7000008458 4 Pcg3381-aspB Pcg1860-pyc 1.00043 0.020083 7000008484 8 Pcg3381-fbp Pcg1860-pyc 0.99686 0.061364 7000008474 8 Pcg3381-ddh Pcg3381-fbp 0.99628 0.019733 7000008522 8 Pcg0755-ptsG Pcg3121-pgi 0.99298 0.066021 7000008528 8 Pcg1860-pyc Pcg3121-pck 0.99129 0.021561 7000008450 4 Pcg1860-asd Pcg3121-pgi 0.98262 0.003107 7000008448 8 Pcg1860-asd Pcg3381-fbp 0.97814 0.022285 7000008494 8 Pcg0007_39- Pcg3381-fbp 0.97407 0.027018 lysE 7000008481 8 Pcg3381-fbp Pcg0007-lysA 0.9694 0.029315 7000008497 8 Pcg0007_39- Pcg1860-pyc 0.9678 0.028569 lysE 7000008507 8 Pcg3121-pgi Pcg3381-fbp 0.96358 0.035078 7000008501 8 Pcg3121-pck Pcg0007-lysA 0.96144 0.018665 7000008486 8 Pcg0007-lysA Pcg0007_265- 0.94523 0.017578 dapB 7000008459 8 Pcg0007_265- Pcg1860-asd 0.94462 0.023847 dapB 7000008506 2 Pcg3121-pgi Pcg0007_265- 0.94345 0.014014 dapD 7000008487 8 Pcg0007-lysA Pcg3381-ddh 0.94249 0.009684 7000008498 8 Pcg3121-pck Pcg1860-asd 0.94154 0.016802 7000008485 8 Pcg0007-lysA Pcg1860-asd 0.94135 0.013578 7000008499 8 Pcg3121-pck Pcg0007_265- 0.93805 0.013317 dapB 7000008472 8 Pcg3381-ddh Pcg1860-asd 0.93716 0.012472 7000008511 8 Pcg0007_39- Pcg1860-asd 0.93673 0.015697 ppc 7000008514 8 Pcg0007_39- Pcg0007-lysA 0.93668 0.027204 ppc 7000008473 8 Pcg3381-ddh Pcg0007_265- 0.93582 0.030377 dapB 7000008461 7 Pcg0007_265- Pcg3381-fbp 0.93498 0.037862 dapB 7000008512 8 Pcg0007_39- Pcg0007_265- 0.93033 0.017521 ppc dapB 7000008456 8 Pcg3381-aspB Pcg3121-pck 0.92544 0.020075 7000008460 8 Pcg0007_265- Pcg0007_265- 0.91723 0.009508 dapB dapD 7000008492 8 Pcg0007_39- Pcg3381-aspB 0.91165 0.012988 lysE 7000008493 8 Pcg0007_39- Pcg0007_265- 0.90609 0.031968 lysE dapD 7000008453 8 Pcg3381-aspB Pcg0007_265- 0.90338 0.013228 dapB 7000008447 8 Pcg1860-asd Pcg0007_265- 0.89886 0.028896 dapD 7000008455 8 Pcg3381-aspB Pcg0007-lysA 0.89531 0.027108 7000008454 6 Pcg3381-aspB Pcg3381-ddh 0.87816 0.025807 7000008523 8 Pcg0755-ptsG Pcg1860-pyc 0.87693 0.030322 7000008520 8 Pcg0755-ptsG Pcg3381-fbp 0.87656 0.018452 7000008533 4 Pcg0007-zwf Pcg3381-fbp 0.84584 0.017012 7000008519 8 Pcg0755-ptsG Pcg0007_265- 0.84196 0.025747 dapD

As predicted by the epistasis model, the second round PRO swap strain comprising the Pcg0007::zwf and Pcg0007::lysA mutations exhibited one of the highest yield improvements, with a nearly 30% improvement in yield over Pcg0007::lysA alone, and a 35.5% improvement over the base strain (see circled data point on FIG. 11).

The HTP methods for exploring solution space of single and double consolidated mutations, can also be applied to third, fourth, and subsequent mutation consolidations. Attention is also drawn, for example, to the disclosed 3-change consolidation strain corresponding to zwf, pyc, and lysa that was made from amongst the top hits of identified in the 2 change consolidations as shown in Table 14 above, and as identified by the epistatic methods of the present disclosure. This 3-change consolidation strain was further validated in tanks as being significantly improved as compared to the parent or parent+zwf (see Table 10 supra, and FIG. 40).

Example 8: HTP Genomic Engineering—Implementation of a Terminator Library to Improve an Industrial Host Strain

The present example applies the HTP methods of the present disclosure to additional HTP genetic design libraries, including STOP swap. The example further illustrates the ability of the present disclosure to combine elements from basic genetic design libraries (e.g., PRO swap, SNP swap, STOP swap, etc.,) to create more complex genetic design libraries (e.g., PRO-STOP swap libraries, incorporating both a promoter and a terminator). In some embodiments, the present disclosure teaches any and all possible genetic design libraries, including those derived from combining any of the previously disclosed genetic design libraries.

In this example, a small scale experiment was conducted to demonstrate the effect of the STOP swap methods of the present invention on gene expression. Terminators T1-T8 of the present disclosure were paired with one of two native Corynebacterium glutamicum promoters as described below, and were analyzed for their ability to impact expression of a fluorescent protein.

A. Assembly of DNA Constructs

Terminators T1-T8 were paired with one of two native Corynebacterium glutamicum promoters (e.g., Pcg0007 or Pcg0047) expressing a yellow fluorescence protein (YFP). To facilitate DNA amplification and assembly, the final promoter-YFP-terminator sequence was synthesized in two portions; the first portion encoded (from 5′ to 3′) i) the vector homology arm, ii) the selected promoter, iii) and ⅔ of the YFP gene. The second portion encoded (from 5′ to 3′) iv) the next ⅔ of the YFP gene, v) the selected terminator, and vi) the second vector homology arm. Each portion was amplified using synthetic oligonucleotides and gel purified. Gel purified amplicons were assembled with a vector backbone using yeast homologous recombination.

B. Transformation of Assembled Clones into E. coli

Vectors containing the Promoter-YFP-terminator sequences were each individually transformed into E. coli in order to identify correctly assembled clones, and to amplify vector DNA for Corynebacterium transformation. Correctly assembled vectors were confirmed by restriction enzyme digest and Sanger sequencing. Positive clones were stored at −20° C. for future use.

C. Transformation of Assembled Clones into Corynebacterium

Verified vector clones were individually transformed into Corynebacterium glutamicum host cells via electroporation. Each vector was designed to integrate into a neutral integration site within the Corynebacterium glutamicum genome that was empirically determined to permit expression of heterologous yellow fluorescence protein but not be detrimental to the host cell. To facilitate integration, the expression vector further comprised about 2 kbp of sequence homologous (i.e., homology arm) to the desired integration site whereby each gene cassette described above was inserted downstream of the homology am. Integration into the genome occurred by single-crossover integration. Transformed Corynebacterium were then tested for correct integration via PCR. This process was repeated for each of the transformations conducted for each gene construct.

D. Evaluation of Individual Terminator Constructs in Corynebacterium

The phenotype of each Corynebacterium transformant containing promoter-YFP-terminator constructs was then tested in two media types (brain heart infusion-BHI and HTP test media) at two time points in order to evaluate expression. Briefly, between four and six PCR-confirmed transformants were chosen and cultivated in selective media in a 96-well format. The initial cultures were then split into selective BHI media or selective seed media. At 48 hours, cultures in seed media were inoculated into selective HTP test media or BHI media and analyzed at two time points representing different portions of the growth curve. Time points for HTP test media cultures were 48 and 96 hours after inoculation. Cultures in the selective BHI media were analyzed at 48 and 72 hours after inoculation.

Analysis of the cultures was performed using a benchtop flow cytometer. Briefly, cultures were diluted 1:100 in 200 μl of phosphate buffered saline (PBS). For each culture, between 3000 and 5000 individual events (i.e., cells) were analyzed for yellow fluorescence. The benchtop flow cytometer plots a histogram of yellow fluorescence of each “event” and calculates the median fluorescence within each well. FIG. 36 depicts the mean of the median fluorescence for each construct (across the 4-6 biological replicates). Error bars indicate the 95% confidence interval of each data point. Conditions A-D each refer to a single media and a single time point. Thus conditions A and B represent the two time points for the BHI media, while the C and D points represent the two time points for the HTP test media. Note that the arbitrary units (e.g., AU) represent the median fluorescence recorded by the benchtop flow cytometer.

The results show that terminators 1-8 of the STOP swap genetic design library result in a continuous range of YFP expression. These terminators thus form a terminator ladder that can be implemented into future genetic design libraries, according to the HTP methods of the present disclosure.

Example 9: Comparing HTP Toolsets vs. Traditional UV Mutations

This example demonstrates the benefits of the HTP genetic design libraries of the present disclosure over traditional mutational strain improvement programs. The experiments in this portion of the specification quantify the improved magnitude and speed of the phenotypical improvements achieved through the HTP methods of the present disclosure over traditional UV mutagenesis.

The present disclosure teaches new methods for accelerating the strain improvement programs of host cells. In some embodiments, the HTP strain improvement program of the present disclosure relies on the ability of the HTP toolsets to generate and identify genetic perturbations. The present inventors attempted to quantify the benefits of the HTP tool sets by conducting a small parallel track strain improvement program comparing the promoter swap techniques of the present disclosure against traditional UV mutations approaches.

A base reference strain producing a biochemical metabolite of interest was chosen as the starting point for both UV and promoter swap genetic perturbations.

A. UV Mutations

Cultures of the base strain were grown in BHI medium in cultures that were OD normalized to OD₆₀₀ of 10. This culture was aliquoted into a sterile petri dish and agitated using a small magnetic stirrer bar. A UV trans illuminator at 254 nm wavelength was then inverted over the culture and aliquots taken at 5 and 9 minutes of UV exposure. These samples were serially diluted 10-fold and each dilution plated onto BHI medium Q-trays. From these Q-trays, approximately 2500 colonies from each UV exposure point were picked using an automated colony picking apparatus and the performance evaluated as below.

B. Promoter Swap

PRO swap constructs were generated in the base strain for 15 gene targets using either all or a subset of promoters selected from P1, P3, P4 and P8 described in Table 1. The final step in the biosynthesis of the product of interest is catalyzed by an O-methyltransferase enzyme that utilizes the potentially rate limiting cofactor S-adenosylmethionine. Gene targets for PRO swaps were therefore selected on the basis that they are directly involved in the biosynthesis of this cofactor or upstream metabolites.

C. UV and Promoter Swap Library Evaluation

The phenotype of each Corynebacterium strain developed for this example was tested for its ability to produce a selected biomolecule. Briefly, between four and six sequence confirmed colonies from each PRO swap strain, and single colonies for each UV strain were chosen and propagated in selective media in a 96-well format in production liquid media.

After biomass propagation in 96-well microwell plates, cell mass was added to fermentation media containing substrate in 96-well microwell plates and bioconversion was allowed to proceed for 24 hrs. Titers of product were determined for each strain using high-performance liquid chromatography from samples taken at 24 hrs. The titer results for each genetic perturbation (UV and PRO swap) was analyzed. Results for each replicate was averaged and assigned to represent the overall performance of said strain. Strains were then binned into categories based on each mutation's effect on measured yield expressed as a ratio over the yield of the base strain.

FIG. 37 summarizes the results of this experiment, which are presented as the number of strains for each strain improvement technique that produced: i) no change in yield, ii) a 1.2 to 1.4 fold improvement to yield, iii) a 1.4 to 1.6 fold improvement to yield, iv) a 1.6 to 1.8 fold improvement to yield, or v) a 1.8 to 2 fold improvement to yield.

The results are illustrative of the benefits of the HTP toolsets of the present disclosure over traditional UV mutagenesis approaches. For example, the results of FIG. 37 demonstrate that the PRO swap strains exhibited a higher rate of positive changes in yield, and were therefore more likely to provide mutations that could significantly improve the strain. Most striking, was the high incidence of high improvement strains showing 1.6, 1.8 and 2 fold increases in the PRO swap library, with little to no identified improvements in the UV library.

The results are also important because they highlight the accelerated rate of improvement of the PRO swap methods of the present disclosure. Indeed, results for the PRO swap library were based on less than 100 promoter::gene perturbations, whereas UV mutation results included the screening of over 4,000 distinct mutant strains. Thus the methods of the present disclosure drastically reduce the number of mutants that must be screened before identifying genetic perturbations capable of conferring strains with high gains in performance.

Example 10: Application of HTP Engineering Methods in Eukaryotes

Previous examples illustrate applications of HTP strain improvement programs on prokaryotic cells. This example demonstrates the applicability of the same techniques to eukaryotic cells. Specifically, Examples 10 and 11 describe a SNP swap strain improvement program for Aspergillus niger for the industrial production of citric acid.

A. Aspergillus Niger Protoplast Formation and Transformation

A large volume (500 ml) of protoplasts of a eukaryotic fungal strain of Aspergillus niger, ATCC 1015, was generated using a commercially available enzyme mixture which contains beta-glucanase activity. The protoplasts were isolated from the enzyme mixture by centrifugation and were ultimately re-suspended in a buffer containing calcium chloride.

The protoplasts were aliquoted and frozen at negative 80 degrees Celsius in containers containing a suspension of dimethyl sulfoxide and polyethylene glycol (PEG). In some embodiments, the present disclosure teaches that a stock of 96-well microtiter plates containing 25-50 microliters of protoplasts in each well can be prepared and frozen in large batches for large scale genome editing campaigns using this technique.

Traditional PEG Calcium mediated transformations were carried out by automated liquid handlers, which combined the DNA with the protoplast-PEG mixtures in the 96 wells. An additional automated liquid handling step was used to plate the transformation on to selective media after transformation.

B. Automated Screening of Transformants

As discussed in more detail below, the A. niger cells had been transformed with a functional pyrG gene, which permitted transformed cells to grow in the absence of Uracil. The pyrG gene of this example was further designed to incorporate into the location of A. niger's wild type aygA gene, thus incorporating a mutation into to the naturally occurring aygA gene. Disruption the aygA gene further results in a yellow spore color, providing a secondary screening method for identifying transformants.

Transformants grown on the selective media without Uracil were isolated and placed into individual wells of a second microtiter plate. The transformants in the second microtiter plate were allowed to grow and sporulate for 2-3 days, before being resuspended in a liquid consisting of water and a small amount of detergent to generate a spore stock suitable for storage and downstream automated screening.

A small aliquot of each of the aforementioned spore stocks was then used to inoculate liquid media in a third 96 well PCR plate. These small cultures are allowed to grow over night in a stationary incubator so that the yellow-pigment containing spores germinate and form hyphae that are more amenable to selection, and downstream steps.

Following the culturing step, the hyphae of the third PCR plate were lysed by adding a commercially available buffer and heating the cultures to 99 degrees Celsius for 20 minutes. The plates were then centrifuged to separate the DNA suspension supernatant from the cell/organelle pellets. The DNA extractions were then used for PCR analysis to identify cell lines comprising the desired DNA modifications.

C. Co-Transformation for Integration of SNPs-Design of SNPs

The DNA sequence of the Aspergillus niger gene aygA was obtained and the proper reading frame was determined. Four distinct types of mutations were designed, which if integrated would result in a null mutation.

The mutations included a single base pair change that incorporates an in-frame stop codon, a small two base pair deletion, a three-base pair integration, and a larger 100 base pair deletion all of which if properly integrated will eliminate aygA activity. Strains lacking aygA activity have a yellow spore phenotype. The designs were generated as in silico constructs that predicted a set of oligomers that were used to build the constructs using Gibson assembly.

D. Integration of SNPs by Co-Transformation

Using the transformation approach described above, amplicons containing the small changes were incorporated into the genome of an Aspergillus niger strain 1015. As previously discussed, this strain of Aspergillus niger comprised a non functional pyrG gene, and was therefore unable to grow in the absence of exogenous uracil. Cells that had successfully integrated the pyrG gene were now capable of growth in the absence of uracil. Of these pyrG+ transformants, isolates that also integrated the small mutations in the aygA gene exhibited the yellow spore phenotype. (FIG. 43A). The presence of the mutation is also detected through Sequencing of small amplicons that contain the region targeted for the SNP exchange (FIG. 43B).

Example 11: HTP Genomic Engineering—Implementation of an HTP SNP Library Strain Improvement Program to Improve Citric Acid Production in Eukaryote Aspergillus niger ATCC11414

Example 10 above described the techniques for automating the genetic engineering techniques of the present disclosure in a high throughput manner. This example applies the techniques described above to the specific HTP strain improvement of Aspergillus niger strain ATCC11414.

Aspergillus niger is a species of filamentous fungi used for the large scale production of citric acid through fermentation. Multiple strains of this species have been isolated and shown to have varying capacity for production of citric and other organic acids. The HTP strain engineering methods of the present disclosure can be used to combine causative alleles and eliminate detrimental alleles to improve citric acid production.

A. Identification of a Library of Genetic Design Library for SNPs from Natural A. niger Strain Variants.

A. niger strain ATCC 1015 was identified as a producer of citric acid in the early twentieth century. An isolate of this strain named ATCC 11414, was later found to exhibit increased citric acid yield over its parent. For example, A. niger strain ATCC 1015 on average produces 7 grams of citric acid from 140 grams of glucose in media containing ammonium nitrate, but lacking both iron and manganese cations. Isolate strain ATCC 11414 on the other hand, exhibits a 10-fold yield increase (70 grams of citric acid) under the same conditions. Moreover, strain ATCC 11414 spores germinate and grow better in citric acid production media than do spores of strain 1015.

In order to identify potential genetic sources for these phenotypic differences, the genomes of both the ATCC 1015 and ATCC 11414 strains were sequenced and analyzed. The resulting analysis identified 42 SNPs distinguishing the 1015 and 11414 strains.

B. Exchanging Causative Alleles

Protoplasts were prepared from strain ATCC 1015 (“base strain”) for transformation. Each of the above-identified 42 SNPs were then individually introduced into the base strain via the gene editing techniques of the present disclosure (“wave up” FIG. 44A). Each SNP was co-transformed with the functional pyrG and aygA gene mutation as described above. Transformants that had successful gene targeting to the aygA locus produced yellow spores (FIG. 44B).

C. Screening for Successful Integration

Transformants containing putative SNPs were isolated and a spore stock was propagated as stated above. Amplicons that contain the region of DNA containing the putative SNP were analyzed by next generation sequencing. Using this approach it is possible to determine successful integration events within each transformant even in the presence of the parental DNA. This capability is essential to determine targeting in fungi which can grow as heterokaryons which contain nuclei with differing genotype in the same cell.

Transformants were further validated for presence of the desired SNP change. The co-transformants that had the yellow spore phenotype also contained proper integration of the citric acid SNP in approximately 30% of the isolates (FIGS. 45 and 46).

The inventors expect to phenotypically screen the created SNP swap microbial strain library, in order to identify SNPs beneficial to the production of citric acid. The inventors will utilize this information, in the context of the HTP methods of genomic engineering described herein, to derive an A. niger strain with increased citric acid production.

Further Embodiments of the Invention

Other subject matter contemplated by the present disclosure is set out in the following numbered embodiments:

-   -   1. A high-throughput (HTP) method of genomic engineering to         evolve a microbe to acquire a desired phenotype, comprising:         -   a. perturbing the genomes of an initial plurality of             microbes having the same microbial strain background, to             thereby create an initial HTP genetic design microbial             strain library comprising individual microbial strains with             unique genetic variations;         -   b. screening and selecting individual microbial strains of             the initial HTP genetic design microbial strain library for             the desired phenotype;         -   c. providing a subsequent plurality of microbes that each             comprise a unique combination of genetic variation, said             genetic variation selected from the genetic variation             present in at least two individual microbial strains             screened in the preceding step, to thereby create a             subsequent HTP genetic design microbial strain library;         -   d. screening and selecting individual microbial strains of             the subsequent HTP genetic design microbial strain library             for the desired phenotype; and         -   e. repeating steps c)-d) one or more times, in a linear or             non-linear fashion, until a microbe has acquired the desired             phenotype, wherein each subsequent iteration creates a new             HTP genetic design microbial strain library comprising             individual microbial strains harboring unique genetic             variations that are a combination of genetic variation             selected from amongst at least two individual microbial             strains of a preceding HTP genetic design microbial strain             library.     -   2. The HTP method of genomic engineering according to embodiment         1, wherein the initial HTP genetic design microbial strain         library comprises at least one selected from the group         consisting of a promoter swap microbial strain library, SNP swap         microbial strain library, start/stop codon microbial strain         library, optimized sequence microbial strain library, a         terminator swap microbial strain library, and any combination         thereof     -   3. The HTP method of genomic engineering according to any one of         embodiments 1-2, wherein the subsequent HTP genetic design         microbial strain library is a full combinatorial microbial         strain library of the initial HTP genetic design microbial         strain library.     -   4. The HTP method of genomic engineering according to any one of         embodiments 1-2, wherein the subsequent HTP genetic design         microbial strain library is a subset of a full combinatorial         microbial strain library of the initial HTP genetic design         microbial strain library.     -   5. The HTP method of genomic engineering according to any one of         embodiments 1-2, wherein the subsequent HTP genetic design         microbial strain library is a full combinatorial microbial         strain library of a preceding HTP genetic design microbial         strain library.     -   6. The HTP method of genomic engineering according to any one of         embodiments 1-5, wherein the subsequent HTP genetic design         microbial strain library is a subset of a full combinatorial         microbial strain library of a preceding HTP genetic design         microbial strain library.     -   7. The HTP method of genomic engineering according to any one of         embodiments 1-5, wherein perturbing the genome comprises         utilizing at least one method selected from the group consisting         of: random mutagenesis, targeted sequence insertions, targeted         sequence deletions, targeted sequence replacements, and any         combination thereof.     -   8. The HTP method of genomic engineering according to any one of         embodiments 1-6, wherein the initial plurality of microbes         comprises unique genetic variations derived from an industrial         production strain microbe.     -   9. The HTP method of genomic engineering according to any one of         embodiments 1-6, wherein the initial plurality of microbes         comprises industrial production strain microbes denoted S₁Gen₁         and any number of subsequent microbial generations derived         therefrom denoted S_(n)Gen_(n).     -   10. A method for generating a SNP swap microbial strain library,         comprising the steps of:         -   a. providing a reference microbial strain and a second             microbial strain, wherein the second microbial strain             comprises a plurality of identified genetic variations             selected from single nucleotide polymorphisms, DNA             insertions, and DNA deletions, which are not present in the             reference microbial strain; and         -   b. perturbing the genome of either the reference microbial             strain, or the second microbial strain, to thereby create an             initial SNP swap microbial strain library comprising a             plurality of individual microbial strains with unique             genetic variations found within each strain of said             plurality of individual microbial strains, wherein each of             said unique genetic variations corresponds to a single             genetic variation selected from the plurality of identified             genetic variations between the reference microbial strain             and the second microbial strain.     -   11. The method for generating a SNP swap microbial strain         library according to embodiment 10, wherein the genome of the         reference microbial strain is perturbed to add one or more of         the identified single nucleotide polymorphisms, DNA insertions,         or DNA deletions, which are found in the second microbial         strain.     -   12. The method for generating a SNP swap microbial strain         library according to embodiment 10, wherein the genome of the         second microbial strain is perturbed to remove one or more of         the identified single nucleotide polymorphisms, DNA insertions,         or DNA deletions, which are not found in the reference microbial         strain.     -   13. The method for generating a SNP swap microbial strain         library according to any one of embodiments 10-12, wherein the         resultant plurality of individual microbial strains with unique         genetic variations, together comprise a full combinatorial         library of all the identified genetic variations between the         reference microbial strain and the second microbial strain.     -   14. The method for generating a SNP swap microbial strain         library according to any one of embodiments 10-12, wherein the         resultant plurality of individual microbial strains with unique         genetic variations, together comprise a subset of a full         combinatorial library of all the identified genetic variations         between the reference microbial strain and the second microbial         strain.     -   15. A method for rehabilitating and improving the phenotypic         performance of an industrial microbial strain, comprising the         steps of:         -   a. providing a parental lineage microbial strain and an             industrial microbial strain derived therefrom, wherein the             industrial microbial strain comprises a plurality of             identified genetic variations selected from single             nucleotide polymorphisms, DNA insertions, and DNA deletions,             not present in the parental lineage microbial strain;         -   b. perturbing the genome of either the parental lineage             microbial strain, or the industrial microbial strain, to             thereby create an initial SNP swap microbial strain library             comprising a plurality of individual microbial strains with             unique genetic variations found within each strain of said             plurality of individual microbial strains, wherein each of             said unique genetic variations corresponds to a single             genetic variation selected from the plurality of identified             genetic variations between the parental lineage microbial             strain and the industrial microbial strain;         -   c. screening and selecting individual microbial strains of             the initial SNP swap microbial strain library for phenotype             performance improvements over a reference microbial strain,             thereby identifying unique genetic variations that confer             said individual microbial strains with phenotype performance             improvements;         -   d. providing a subsequent plurality of microbes that each             comprise a unique combination of genetic variation, said             genetic variation selected from the genetic variation             present in at least two individual microbial strains             screened in the preceding step, to thereby create a             subsequent SNP swap microbial strain library;         -   e. screening and selecting individual microbial strains of             the subsequent SNP swap microbial strain library for             phenotype performance improvements over the reference             microbial strain, thereby identifying unique combinations of             genetic variation that confer said microbial strains with             additional phenotype performance improvements; and         -   f. repeating steps d)-e) one or more times, in a linear or             non-linear fashion, until a microbial strain exhibits a             desired level of improved phenotype performance compared to             the phenotype performance of the industrial microbial             strain, wherein each subsequent iteration creates a new SNP             swap microbial strain library comprising individual             microbial strains harboring unique genetic variations that             are a combination of genetic variation selected from amongst             at least two individual microbial strains of a preceding SNP             swap microbial strain library.     -   15.1. The method for rehabilitating and improving the phenotypic         performance of an industrial microbial strain according to         embodiment 15, wherein the identified genetic variations further         comprise artificial promoter swap genetic variations from a         promoter swap library.     -   16. The method for rehabilitating and improving the phenotypic         performance of an industrial microbial strain according to any         one of embodiments 15-15.1, wherein the resultant plurality of         individual microbial strains with unique genetic variations,         together comprise a full combinatorial library of all the         identified genetic variations between the reference microbial         strain and the second microbial strain.     -   17. The method for rehabilitating and improving the phenotypic         performance of an industrial microbial strain according to any         one of embodiments 15-15.1, wherein the resultant plurality of         individual microbial strains with unique genetic variations,         together comprise a subset of a full combinatorial library of         all the identified genetic variations between the reference         microbial strain and the second microbial strain.     -   18. The method for rehabilitating and improving the phenotypic         performance of an industrial microbial strain according to any         one of embodiments 15-17, wherein the resultant subsequent         plurality of individual microbial strains with unique         combinations of genetic variations, together comprise a subset         of a full combinatorial library of all the genetic variations         present in the individual microbial strains screened in the         preceding step.     -   19. The method for rehabilitating and improving the phenotypic         performance of an industrial microbial strain according to any         one of embodiments 15-18, wherein the genome of the parental         lineage microbial strain is perturbed to add one or more of the         identified single nucleotide polymorphisms, DNA insertions, or         DNA deletions, which are found in the industrial microbial         strain.     -   20. The method for rehabilitating and improving the phenotypic         performance of an industrial microbial strain according to any         one of embodiments 15-18, wherein the genome of the industrial         microbial strain is perturbed to remove one or more of the         identified single nucleotide polymorphisms, DNA insertions, or         DNA deletions, which are not found in the parental lineage         microbial strain.     -   21. A method for generating a promoter swap microbial strain         library, said method comprising the steps of:         -   a. providing a plurality of target genes endogenous to a             base microbial strain, and a promoter ladder, wherein said             promoter ladder comprises a plurality of promoters             exhibiting different expression profiles in the base             microbial strain; and         -   b. engineering the genome of the base microbial strain, to             thereby create an initial promoter swap microbial strain             library comprising a plurality of individual microbial             strains with unique genetic variations found within each             strain of said plurality of individual microbial strains,             wherein each of said unique genetic variations comprises one             or more of the promoters from the promoter ladder operably             linked to one of the target genes endogenous to the base             microbial strain.     -   22. A promoter swap method of genomic engineering to evolve a         microbe to acquire a desired phenotype, said method comprising         the steps of:         -   a. providing a plurality of target genes endogenous to a             base microbial strain, and a promoter ladder, wherein said             promoter ladder comprises a plurality of promoters             exhibiting different expression profiles in the base             microbial strain;         -   b. engineering the genome of the base microbial strain, to             thereby create an initial promoter swap microbial strain             library comprising a plurality of individual microbial             strains with unique genetic variations found within each             strain of said plurality of individual microbial strains,             wherein each of said unique genetic variations comprises one             or more of the promoters from the promoter ladder operably             linked to one of the target genes endogenous to the base             microbial strain;         -   c. screening and selecting individual microbial strains of             the initial promoter swap microbial strain library for the             desired phenotype;         -   d. providing a subsequent plurality of microbes that each             comprise a unique combination of genetic variation, said             genetic variation selected from the genetic variation             present in at least two individual microbial strains             screened in the preceding step, to thereby create a             subsequent promoter swap microbial strain library;         -   e. screening and selecting individual microbial strains of             the subsequent promoter swap microbial strain library for             the desired phenotype; and         -   f. repeating steps d)-e) one or more times, in a linear or             non-linear fashion, until a microbe has acquired the desired             phenotype, wherein each subsequent iteration creates a new             promoter swap microbial strain library comprising individual             microbial strains harboring unique genetic variations that             are a combination of genetic variation selected from amongst             at least two individual microbial strains of a preceding             promoter swap microbial strain library.     -   23. The promoter swap method of genomic engineering to evolve a         microbe to acquire a desired phenotype according to embodiment         22, wherein the resultant subsequent plurality of individual         microbial strains with unique combinations of genetic         variations, together comprise a subset of a full combinatorial         library of all the genetic variations present in the individual         microbial strains screened in the preceding step.     -   23.1. The promoter swap method of genomic engineering to evolve         a microbe to acquire a desired phenotype according to embodiment         22, wherein the resultant subsequent plurality of individual         microbial strains with unique combinations of genetic         variations, together comprise a full combinatorial library of         all the genetic variations present in the individual microbial         strains screened in the preceding step.     -   24. A method for generating a terminator swap microbial strain         library, said method comprising the steps of:         -   a. providing a plurality of target genes endogenous to a             base microbial strain, and a terminator ladder, wherein said             terminator ladder comprises a plurality of terminators             exhibiting different expression profiles in the base             microbial strain; and         -   b. engineering the genome of the base microbial strain, to             thereby create an initial terminator swap microbial strain             library comprising a plurality of individual microbial             strains with unique genetic variations found within each             strain of said plurality of individual microbial strains,             wherein each of said unique genetic variations comprises one             of the target genes endogenous to the base microbial strain             operably linked to one or more of the terminators from the             terminator ladder.     -   25. A terminator swap method of genomic engineering to evolve a         microbe to acquire a desired phenotype, said method comprising         the steps of:         -   a. providing a plurality of target genes endogenous to a             base microbial strain, and a terminator ladder, wherein said             terminator ladder comprises a plurality of terminators             exhibiting different expression profiles in the base             microbial strain;         -   b. engineering the genome of the base microbial strain, to             thereby create an initial terminator swap microbial strain             library comprising a plurality of individual microbial             strains with unique genetic variations found within each             strain of said plurality of individual microbial strains,             wherein each of said unique genetic variations comprises one             of the target genes endogenous to the base microbial strain             operably linked to one or more of the terminators from the             terminator ladder;         -   c. screening and selecting individual microbial strains of             the initial terminator swap microbial strain library for the             desired phenotype;         -   d. providing a subsequent plurality of microbes that each             comprise a unique combination of genetic variation, said             genetic variation selected from the genetic variation             present in at least two individual microbial strains             screened in the preceding step, to thereby create a             subsequent terminator swap microbial strain library;         -   e. screening and selecting individual microbial strains of             the subsequent terminator swap microbial strain library for             the desired phenotype; and         -   f. repeating steps d)-e) one or more times, in a linear or             non-linear fashion, until a microbe has acquired the desired             phenotype, wherein each subsequent iteration creates a new             terminator swap microbial strain library comprising             individual microbial strains harboring unique genetic             variations that are a combination of genetic variation             selected from amongst at least two individual microbial             strains of a preceding terminator swap microbial strain             library.     -   26. The terminator swap method of genomic engineering to evolve         a microbe to acquire a desired phenotype according to embodiment         25, wherein the resultant subsequent plurality of individual         microbial strains with unique combinations of genetic         variations, together comprise a subset of a full combinatorial         library of all the genetic variations present in the individual         microbial strains screened in the preceding step.     -   26.1. The terminator swap method of genomic engineering to         evolve a microbe to acquire a desired phenotype according to         embodiment 25, wherein the resultant subsequent plurality of         individual microbial strains with unique combinations of genetic         variations, together comprise a full combinatorial library of         all the genetic variations present in the individual microbial         strains screened in the preceding step.     -   27. A high-throughput (HTP) genomic engineering system for         evolving a microbe to acquire         -   a desired phenotype, the system comprising:             -   one or more processors; and             -   one or more memories operatively coupled to at least one                 of the one or more processors and having instructions                 stored thereon that, when executed by at least one of                 the one or more processors, cause the system to:             -   a. perturb the genomes of an initial plurality of                 microbes having the same microbial strain background, to                 thereby create an initial HTP genetic design microbial                 strain library comprising individual microbial strains                 with unique genetic variations;             -   b. screen and select individual microbial strains of the                 initial HTP genetic design microbial strain library for                 the desired phenotype;             -   c. provide a subsequent plurality of microbes that each                 comprise a unique combination of genetic variation, said                 genetic variation selected from the genetic variation                 present in at least two individual microbial strains                 screened in the preceding step, to thereby create a                 subsequent HTP genetic design microbial strain library;             -   d. screen and select individual microbial strains of the                 subsequent HTP genetic design microbial strain library                 for the desired phenotype; and             -   e. repeat steps c)-d) one or more times, in a linear or                 non-linear fashion, until a microbe has acquired the                 desired phenotype, wherein each subsequent iteration                 creates a new HTP genetic design microbial strain                 library comprising individual microbial strains                 harboring unique genetic variations that are a                 combination of genetic variation selected from amongst                 at least two individual microbial strains of a preceding                 HTP genetic design microbial strain library.     -   28. One or more non-transitory computer readable media storing         instructions for evolving a microbe to acquire a desired         phenotype, wherein the instructions, when executed by one or         more computing devices, cause at least one of the one or more         computing devices to:         -   a. perturb the genomes of an initial plurality of microbes             having the same microbial strain background, to thereby             create an initial HTP genetic design microbial strain             library comprising individual microbial strains with unique             genetic variations;         -   b. screen and select individual microbial strains of the             initial HTP genetic design microbial strain library for the             desired phenotype;         -   c. provide a subsequent plurality of microbes that each             comprise a unique combination of genetic variation, said             genetic variation selected from the genetic variation             present in at least two individual microbial strains             screened in the preceding step, to thereby create a             subsequent HTP genetic design microbial strain library;         -   d. screen and select individual microbial strains of the             subsequent HTP genetic design microbial strain library for             the desired phenotype; and         -   e. repeat steps c)-d) one or more times, in a linear or             non-linear fashion, until a microbe has acquired the desired             phenotype, wherein each subsequent iteration creates a new             HTP genetic design microbial strain library comprising             individual microbial strains harboring unique genetic             variations that are a combination of genetic variation             selected from amongst at least two individual microbial             strains of a preceding HTP genetic design microbial strain             library.     -   29. A system for generating a SNP swap microbial strain library,         the system comprising:         -   one or more processors; and         -   one or more memories operatively coupled to at least one of             the one or more processors and having instructions stored             thereon that, when executed by at least one of the one or             more processors, cause the system to:         -   a. provide a reference microbial strain and a second             microbial strain, wherein the second microbial strain             comprises a plurality of identified genetic variations             selected from single nucleotide polymorphisms, DNA             insertions, and DNA deletions, which are not present in the             reference microbial strain; and         -   b. perturb the genome of either the reference microbial             strain, or the second microbial strain, to thereby create an             initial SNP swap microbial strain library comprising a             plurality of individual microbial strains with unique             genetic variations found within each strain of said             plurality of individual microbial strains, wherein each of             said unique genetic variations corresponds to a single             genetic variation selected from the plurality of identified             genetic variations between the reference microbial strain             and the second microbial strain.     -   30. One or more non-transitory computer readable media storing         instructions for generating a SNP swap microbial strain library,         wherein the instructions, when executed by one or more computing         devices, cause at least one of the one or more computing devices         to:         -   a. provide a reference microbial strain and a second             microbial strain, wherein the second microbial strain             comprises a plurality of identified genetic variations             selected from single nucleotide polymorphisms, DNA             insertions, and DNA deletions, which are not present in the             reference microbial strain; and         -   b. perturb the genome of either the reference microbial             strain, or the second microbial strain, to thereby create an             initial SNP swap microbial strain library comprising a             plurality of individual microbial strains with unique             genetic variations found within each strain of said             plurality of individual microbial strains, wherein each of             said unique genetic variations corresponds to a single             genetic variation selected from the plurality of identified             genetic variations between the reference microbial strain             and the second microbial strain.     -   31. A system for rehabilitating and improving the phenotypic         performance of an industrial microbial strain, the system         comprising:         -   one or more processors; and         -   one or more memories operatively coupled to at least one of             the one or more processors and having instructions stored             thereon that, when executed by at least one of the one or             more processors, cause the system to:         -   a. provide a parental lineage microbial strain and an             industrial microbial strain derived therefrom, wherein the             industrial microbial strain comprises a plurality of             identified genetic variations selected from single             nucleotide polymorphisms, DNA insertions, and DNA deletions,             not present in the parental lineage microbial strain;         -   b. perturb the genome of either the parental lineage             microbial strain, or the industrial microbial strain, to             thereby create an initial SNP swap microbial strain library             comprising a plurality of individual microbial strains with             unique genetic variations found within each strain of said             plurality of individual microbial strains, wherein each of             said unique genetic variations corresponds to a single             genetic variation selected from the plurality of identified             genetic variations between the parental lineage microbial             strain and the industrial microbial strain;         -   c. screen and select individual microbial strains of the             initial SNP swap microbial strain library for phenotype             performance improvements over a reference microbial strain,             thereby identifying unique genetic variations that confer             said microbial strains with phenotype performance             improvements;         -   d. provide a subsequent plurality of microbes that each             comprise a unique combination of genetic variation, said             genetic variation selected from the genetic variation             present in at least two individual microbial strains             screened in the preceding step, to thereby create a             subsequent SNP swap microbial strain library;         -   e. screen and select individual microbial strains of the             subsequent SNP swap microbial strain library for phenotype             performance improvements over the reference microbial             strain, thereby identifying unique combinations of genetic             variation that confer said microbial strains with additional             phenotype performance improvements; and         -   f. repeat steps d)-e) one or more times, in a linear or             non-linear fashion, until a microbial strain exhibits a             desired level of improved phenotype performance compared to             the phenotype performance of the industrial microbial             strain, wherein each subsequent iteration creates a new SNP             swap microbial strain library comprising individual             microbial strains harboring unique genetic variations that             are a combination of genetic variation selected from amongst             at least two individual microbial strains of a preceding SNP             swap microbial strain library.     -   32. One or more non-transitory computer readable media storing         instructions for rehabilitating and improving the phenotypic         performance of an industrial microbial strain, wherein the         instructions, when executed by one or more computing devices,         cause at least one of the one or more computing devices to:         -   a. provide a parental lineage microbial strain and an             industrial microbial strain derived therefrom, wherein the             industrial microbial strain comprises a plurality of             identified genetic variations selected from single             nucleotide polymorphisms, DNA insertions, and DNA deletions,             not present in the parental lineage microbial strain;         -   b. perturb the genome of either the parental lineage             microbial strain, or the industrial microbial strain, to             thereby create an initial SNP swap microbial strain library             comprising a plurality of individual microbial strains with             unique genetic variations found within each strain of said             plurality of individual microbial strains, wherein each of             said unique genetic variations corresponds to a single             genetic variation selected from the plurality of identified             genetic variations between the parental lineage microbial             strain and the industrial microbial strain;         -   c. screen and select individual microbial strains of the             initial SNP swap microbial strain library for phenotype             performance improvements over a reference microbial strain,             thereby identifying unique genetic variations that confer             said microbial strains with phenotype performance             improvements;         -   d. provide a subsequent plurality of microbes that each             comprise a unique combination of genetic variation, said             genetic variation selected from the genetic variation             present in at least two individual microbial strains             screened in the preceding step, to thereby create a             subsequent SNP swap microbial strain library;         -   e. screen and select individual microbial strains of the             subsequent SNP swap microbial strain library for phenotype             performance improvements over the reference microbial             strain, thereby identifying unique combinations of genetic             variation that confer said microbial strains with additional             phenotype performance improvements; and         -   f. repeat steps d)-e) one or more times, in a linear or             non-linear fashion, until a microbial strain exhibits a             desired level of improved phenotype performance compared to             the phenotype performance of the industrial microbial             strain, wherein each subsequent iteration creates a new SNP             swap microbial strain library comprising individual             microbial strains harboring unique genetic variations that             are a combination of genetic variation selected from amongst             at least two individual microbial strains of a preceding SNP             swap microbial strain library.     -   33. A system for generating a promoter swap microbial strain         library, the system comprising:         -   one or more processors; and         -   one or more memories operatively coupled to at least one of             the one or more processors and having instructions stored             thereon that, when executed by at least one of the one or             more processors, cause the system to:         -   a. provide a plurality of target genes endogenous to a base             microbial strain, and a promoter ladder, wherein said             promoter ladder comprises a plurality of promoters             exhibiting different expression profiles in the base             microbial strain; and         -   b. engineer the genome of the base microbial strain, to             thereby create an initial promoter swap microbial strain             library comprising a plurality of individual microbial             strains with unique genetic variations found within each             strain of said plurality of individual microbial strains,             wherein each of said unique genetic variations comprises one             or more of the promoters from the promoter ladder operably             linked to one of the target genes endogenous to the base             microbial strain.     -   34. One or more non-transitory computer readable media storing         instructions for generating a promoter swap microbial strain         library, wherein the instructions, when executed by one or more         computing devices, cause at least one of the one or more         computing devices to:         -   a. provide a plurality of target genes endogenous to a base             microbial strain, and a promoter ladder, wherein said             promoter ladder comprises a plurality of promoters             exhibiting different expression profiles in the base             microbial strain; and         -   b. engineer the genome of the base microbial strain, to             thereby create an initial promoter swap microbial strain             library comprising a plurality of individual microbial             strains with unique genetic variations found within each             strain of said plurality of individual microbial strains,             wherein each of said unique genetic variations comprises one             or more of the promoters from the promoter ladder operably             linked to one of the target genes endogenous to the base             microbial strain.     -   35. A genomic engineering system to evolve a microbe through         promoter swapping to acquire a desired phenotype, the system         comprising:         -   one or more processors; and         -   one or more memories operatively coupled to at least one of             the one or more processors and having instructions stored             thereon that, when executed by at least one of the one or             more processors, cause the system to:         -   a. provide a plurality of target genes endogenous to a base             microbial strain, and a promoter ladder, wherein said             promoter ladder comprises a plurality of promoters             exhibiting different expression profiles in the base             microbial strain;         -   b. engineer the genome of the base microbial strain, to             thereby create an initial promoter swap microbial strain             library comprising a plurality of individual microbial             strains with unique genetic variations found within each             strain of said plurality of individual microbial strains,             wherein each of said unique genetic variations comprises one             or more of the promoters from the promoter ladder operably             linked to one of the target genes endogenous to the base             microbial strain;         -   c. screen and select individual microbial strains of the             initial promoter swap microbial strain library for the             desired phenotype;         -   d. provide a subsequent plurality of microbes that each             comprise a unique combination of genetic variation, said             genetic variation selected from the genetic variation             present in at least two individual microbial strains             screened in the preceding step, to thereby create a             subsequent promoter swap microbial strain library;         -   e. screen and select individual microbial strains of the             subsequent promoter swap microbial strain library for the             desired phenotype; and         -   f. repeat steps d)-e) one or more times, in a linear or             non-linear fashion, until a microbe has acquired the desired             phenotype, wherein each subsequent iteration creates a new             promoter swap microbial strain library comprising individual             microbial strains harboring unique genetic variations that             are a combination of genetic variation selected from amongst             at least two individual microbial strains of a preceding             promoter swap microbial strain library.     -   36. One or more non-transitory computer readable media storing         instructions for evolving a microbe through promoter swapping to         acquire a desired phenotype, wherein the instructions, when         executed by one or more computing devices, cause at least one of         the one or more computing devices to:         -   a. provide a plurality of target genes endogenous to a base             microbial strain, and a promoter ladder, wherein said             promoter ladder comprises a plurality of promoters             exhibiting different expression profiles in the base             microbial strain;         -   b. engineer the genome of the base microbial strain, to             thereby create an initial promoter swap microbial strain             library comprising a plurality of individual microbial             strains with unique genetic variations found within each             strain of said plurality of individual microbial strains,             wherein each of said unique genetic variations comprises one             or more of the promoters from the promoter ladder operably             linked to one of the target genes endogenous to the base             microbial strain;         -   c. screen and select individual microbial strains of the             initial promoter swap microbial strain library for the             desired phenotype;         -   d. provide a subsequent plurality of microbes that each             comprise a unique combination of genetic variation, said             genetic variation selected from the genetic variation             present in at least two individual microbial strains             screened in the preceding step, to thereby create a             subsequent promoter swap microbial strain library;         -   e. screen and select individual microbial strains of the             subsequent promoter swap microbial strain library for the             desired phenotype; and         -   f. repeat steps d)-e) one or more times, in a linear or             non-linear fashion, until a microbe has acquired the desired             phenotype, wherein each subsequent iteration creates a new             promoter swap microbial strain library comprising individual             microbial strains harboring unique genetic variations that             are a combination of genetic variation selected from amongst             at least two individual microbial strains of a preceding             promoter swap microbial strain library.     -   37. A system for generating a terminator swap microbial strain         library, the system comprising:         -   one or more processors; and         -   one or more memories operatively coupled to at least one of             the one or more processors and having instructions stored             thereon that, when executed by at least one of the one or             more processors, cause the system to:         -   a. provide a plurality of target genes endogenous to a base             microbial strain, and a terminator ladder, wherein said             terminator ladder comprises a plurality of terminators             exhibiting different expression profiles in the base             microbial strain; and         -   b. engineer the genome of the base microbial strain, to             thereby create an initial terminator swap microbial strain             library comprising a plurality of individual microbial             strains with unique genetic variations found within each             strain of said plurality of individual microbial strains,             wherein each of said unique genetic variations comprises one             of the target genes endogenous to the base microbial strain             operably linked to one or more of the terminators from the             terminator ladder.     -   38. One or more non-transitory computer readable media storing         instructions for generating a terminator swap microbial strain         library, wherein the instructions, when executed by one or more         computing devices, cause at least one of the one or more         computing devices to:         -   a. provide a plurality of target genes endogenous to a base             microbial strain, and a terminator ladder, wherein said             terminator ladder comprises a plurality of terminators             exhibiting different expression profiles in the base             microbial strain; and         -   b. engineer the genome of the base microbial strain, to             thereby create an initial terminator swap microbial strain             library comprising a plurality of individual microbial             strains with unique genetic variations found within each             strain of said plurality of individual microbial strains,             wherein each of said unique genetic variations comprises one             of the target genes endogenous to the base microbial strain             operably linked to one or more of the terminators from the             terminator ladder.     -   39. A genomic engineering system to evolve through terminator         swapping a microbe to acquire a desired phenotype, the system         comprising:         -   one or more processors; and         -   one or more memories operatively coupled to at least one of             the one or more processors and having instructions stored             thereon that, when executed by at least one of the one or             more processors, cause the system to:         -   a. provide a plurality of target genes endogenous to a base             microbial strain, and a terminator ladder, wherein said             terminator ladder comprises a plurality of terminators             exhibiting different expression profiles in the base             microbial strain;         -   b. engineer the genome of the base microbial strain, to             thereby create an initial terminator swap microbial strain             library comprising a plurality of individual microbial             strains with unique genetic variations found within each             strain of said plurality of individual microbial strains,             wherein each of said unique genetic variations comprises one             of the target genes endogenous to the base microbial strain             operably linked to one or more of the terminators from the             terminator ladder;         -   c. screen and select individual microbial strains of the             initial terminator swap microbial strain library for the             desired phenotype;         -   d. provide a subsequent plurality of microbes that each             comprise a unique combination of genetic variation, said             genetic variation selected from the genetic variation             present in at least two individual microbial strains             screened in the preceding step, to thereby create a             subsequent terminator swap microbial strain library;         -   e. screen and select individual microbial strains of the             subsequent terminator swap microbial strain library for the             desired phenotype; and         -   f. repeat steps d)-e) one or more times, in a linear or             non-linear fashion, until a microbe has acquired the desired             phenotype, wherein each subsequent iteration creates a new             terminator swap microbial strain library comprising             individual microbial strains harboring unique genetic             variations that are a combination of genetic variation             selected from amongst at least two individual microbial             strains of a preceding terminator swap microbial strain             library.     -   40. One or more non-transitory computer readable media storing         instructions for evolving through terminator swapping a microbe         to acquire a desired phenotype, wherein the instructions, when         executed by one or more computing devices, cause at least one of         the one or more computing devices to:         -   a. provide a plurality of target genes endogenous to a base             microbial strain, and a terminator ladder, wherein said             terminator ladder comprises a plurality of terminators             exhibiting different expression profiles in the base             microbial strain;         -   b. engineer the genome of the base microbial strain, to             thereby create an initial terminator swap microbial strain             library comprising a plurality of individual microbial             strains with unique genetic variations found within each             strain of said plurality of individual microbial strains,             wherein each of said unique genetic variations comprises one             of the target genes endogenous to the base microbial strain             operably linked to one or more of the terminators from the             terminator ladder;         -   c. screen and select individual microbial strains of the             initial terminator swap microbial strain library for the             desired phenotype;         -   d. provide a subsequent plurality of microbes that each             comprise a unique combination of genetic variation, said             genetic variation selected from the genetic variation             present in at least two individual microbial strains             screened in the preceding step, to thereby create a             subsequent terminator swap microbial strain library;         -   e. screen and select individual microbial strains of the             subsequent terminator swap microbial strain library for the             desired phenotype; and         -   f. repeat steps d)-e) one or more times, in a linear or             non-linear fashion, until a microbe has acquired the desired             phenotype, wherein each subsequent iteration creates a new             terminator swap microbial strain library comprising             individual microbial strains harboring unique genetic             variations that are a combination of genetic variation             selected from amongst at least two individual microbial             strains of a preceding terminator swap microbial strain             library.     -   41. A computer-implemented method for iteratively improving the         design of candidate microbial strains, the method comprising:         -   a. accessing a predictive model populated with a training             set comprising (1) inputs representing genetic changes to             one or more background microbial strains and (2)             corresponding performance measures;         -   b. applying test inputs to the predictive model that             represent genetic changes, the test inputs corresponding to             candidate microbial strains incorporating those genetic             changes;         -   c. predicting phenotypic performance of the candidate             microbial strains based at least in part upon the predictive             model;         -   d. selecting a first subset of the candidate microbial             strains based at least in part upon their predicted             performance;         -   e. obtaining measured phenotypic performance of the first             subset of the candidate microbial strains;         -   f. obtaining a selection of a second subset of the candidate             microbial strains based at least in part upon their measured             phenotypic performance;         -   g. adding to the training set of the predictive model (1)             inputs corresponding to the selected second subset of             candidate microbial strains, along with (2) corresponding             measured performance of the selected second subset of             candidate microbial strains; and         -   h. repeating (b)-(g).     -   42. The method of embodiment 41, wherein repeating (b)-(g)         comprises repeating (b)-(g) until measured phenotypic         performance of at least one candidate microbial strain satisfies         a performance metric.     -   43. The method of embodiment 41, wherein:         -   during a first application of test inputs to the predictive             model, the genetic changes represented by the test inputs             comprise genetic changes to the one or more background             microbial strains; and         -   during subsequent applications of test inputs, the genetic             changes represented by the test inputs comprise genetic             changes to candidate microbial strains within a previously             selected second subset of candidate microbial strains.     -   44. The method of embodiment 41, wherein the selection of the         first subset of the candidate microbial strains is based at         least in part upon epistatic effects.     -   45. The method of embodiment 44, wherein the selection of the         first subset based at least in part upon epistatic effects         comprises:         -   during a first selection of the first subset:         -   determining degrees of dissimilarity between performance             measures of the one or more background microbial strains in             response to application of a plurality of respective inputs             representing genetic changes to the one or more background             microbial strains; and         -   selecting for inclusion in the first subset at least two             candidate microbial strains based at least in part upon the             degrees of dissimilarity in the performance measures of the             one or more background microbial strains in response to             application of genetic changes incorporated into the at             least two candidate microbial strains.     -   46. The method of embodiment 45, further comprising:         -   during subsequent selections of the first subset:         -   determining degrees of dissimilarity between performance             measures of previous first subset candidate microbial             strains in response to application of a plurality of             respective inputs representing genetic changes, wherein the             previous first subset candidate microbial strains are             strains that were selected during a previous selection of             the first subset; and         -   selecting for inclusion into the first subset at least two             candidate microbial strains based at least in part upon the             degrees of dissimilarity in the performance measures of the             previous first subset candidate microbial strains in             response to application of the genetic changes incorporated             into the at least two candidate microbial strains.     -   47. A system for iteratively improving the design of candidate         microbial strains, the system comprising:         -   one or more processors; and         -   one or more memories operatively coupled to at least one of             the one or more processors and having instructions stored             thereon that, when executed by at least one of the one or             more processors, cause the system to:             -   a. access a predictive model populated with a training                 set comprising (1) inputs representing genetic changes                 to one or more background microbial strains and (2)                 corresponding performance measures;             -   b. apply test inputs to the predictive model that                 represent genetic changes, the test inputs corresponding                 to candidate microbial strains incorporating those                 genetic changes;             -   c. predict phenotypic performance of the candidate                 microbial strains based at least in part upon the                 predictive model;             -   d. select a first subset of the candidate microbial                 strains based at least in part upon their predicted                 performance;             -   e. obtain measured phenotypic performance of the first                 subset of the candidate microbial strains;             -   f. obtain a selection of a second subset of the                 candidate microbial strains based at least in part upon                 their measured phenotypic performance;             -   g. add to the training set of the predictive model (1)                 inputs corresponding to the selected second subset of                 candidate microbial strains, along with (2)                 corresponding measured performance of the selected                 second subset of candidate microbial strains; and             -   h. repeat (b)-(g).     -   48. The system of embodiment 47, wherein the instructions, when         executed by at least one of the one or more processors, cause         the system to repeat (b)-(g) until measured phenotypic         performance of at least one candidate microbial strain satisfies         a performance metric.     -   49. The system of embodiment 47, wherein:         -   during a first application of test inputs to the predictive             model, the genetic changes represented by the test inputs             comprise genetic changes to the one or more background             microbial strains; and         -   during subsequent applications of test inputs, the genetic             changes represented by the test inputs comprise genetic             changes to candidate microbial strains within a previously             selected second subset of candidate microbial strains.     -   50. The system of embodiment 47, wherein the selection of the         first subset of the candidate microbial strains is based at         least in part upon epistatic effects.     -   51. The system of embodiment 50, wherein the instructions, when         executed by at least one of the one or more processors, cause         the system, during a first selection of the first subset, to:         -   determine degrees of dissimilarity between performance             measures of the one or more background microbial strains in             response to application of a plurality of respective inputs             representing genetic changes to the one or more background             microbial strains; and         -   select for inclusion in the first subset at least two             candidate microbial strains based at least in part upon the             degrees of dissimilarity in the performance measures of the             one or more background microbial strains in response to             application of genetic changes incorporated into the at             least two candidate microbial strains.     -   52. The system of embodiment 51, wherein the instructions, when         executed by at least one of the one or more processors, cause         the system, during subsequent selections of the first subset,         to:         -   determine degrees of dissimilarity between performance             measures of previous first subset candidate microbial             strains in response to application of a plurality of             respective inputs representing genetic changes, wherein the             previous first subset candidate microbial strains are             strains that were selected during a previous selection of             the first subset; and         -   select for inclusion into the first subset at least two             candidate microbial strains based at least in part upon the             degrees of dissimilarity in the performance measures of the             previous first subset candidate microbial strains in             response to application of the genetic changes incorporated             into the at least two candidate microbial strains.     -   53. One or more non-transitory computer readable media storing         instructions for iteratively improving the design of candidate         microbial strains, wherein the instructions, when executed by         one or more computing devices, cause at least one of the one or         more computing devices to:         -   a. access a predictive model populated with a training set             comprising (1) inputs representing genetic changes to one or             more background microbial strains and (2) corresponding             performance measures;         -   b. apply test inputs to the predictive model that represent             genetic changes, the test inputs corresponding to candidate             microbial strains incorporating those genetic changes;         -   c. predict phenotypic performance of the candidate microbial             strains based at least in part upon the predictive model;         -   d. select a first subset of the candidate microbial strains             based at least in part upon their predicted performance;         -   e. obtain measured phenotypic performance of the first             subset of the candidate microbial strains;         -   f. obtain a selection of a second subset of the candidate             microbial strains based at least in part upon their measured             phenotypic performance;         -   g. add to the training set of the predictive model (1)             inputs corresponding to the selected second subset of             candidate microbial strains, along with (2) corresponding             measured performance of the selected second subset of             candidate microbial strains; and         -   h. repeat (b)-(g).     -   54. The computer readable media of embodiment 53, wherein the         instructions, when executed, cause at least one of the one or         more computing devices to repeat (b)-(g) until measured         phenotypic performance of at least one candidate microbial         strain satisfies a performance metric.     -   55. The computer readable media of embodiment 53, wherein:         -   during a first application of test inputs to the predictive             model, the genetic changes represented by the test inputs             comprise genetic changes to the one or more background             microbial strains; and         -   during subsequent applications of test inputs, the genetic             changes represented by the test inputs comprise genetic             changes to candidate microbial strains within a previously             selected second subset of candidate microbial strains.     -   56. The computer readable media of embodiment 53, wherein the         selection of the first subset of the candidate microbial strains         is based at least in part upon epistatic effects.     -   57. The computer readable media of embodiment 56, wherein the         instructions, when executed, cause at least one of the one or         more computing devices, during a first selection of the first         subset, to:         -   determine degrees of dissimilarity between performance             measures of the one or more background microbial strains in             response to application of a plurality of respective inputs             representing genetic changes to the one or more background             microbial strains; and         -   select for inclusion in the first subset at least two             candidate microbial strains based at least in part upon the             degrees of dissimilarity in the performance measures of the             one or more background microbial strains in response to             application of genetic changes incorporated into the at             least two candidate microbial strains.     -   58. The computer readable media of embodiment 53, wherein the         instructions, when executed, cause at least one of the one or         more computing devices, during subsequent selections of the         first subset, to:         -   determine degrees of dissimilarity between performance             measures of previous first subset candidate microbial             strains in response to application of a plurality of             respective inputs representing genetic changes, wherein the             previous first subset candidate microbial strains are             strains that were selected during a previous selection of             the first subset; and         -   select for inclusion into the first subset at least two             candidate microbial strains based at least in part upon the             degrees of dissimilarity in the performance measures of the             previous first subset candidate microbial strains in             response to application of the genetic changes incorporated             into the at least two candidate microbial strains.     -   59. A computer-implemented method for applying epistatic effects         in the iterative improvement of candidate microbial strains, the         method comprising:         -   obtaining data representing measured performance in response             to corresponding genetic changes made to at least one             microbial background strain;         -   obtaining a selection of at least two genetic changes based             at least in part upon a degree of dissimilarity between the             corresponding responsive performance measures of the at             least two genetic changes,         -   wherein the degree of dissimilarity relates to the degree to             which the at least two genetic changes affect their             corresponding responsive performance measures through             different biological pathways; and         -   designing genetic changes to a microbial background strain             that include the selected genetic changes.     -   60. The method of embodiment 59, wherein the microbial         background strain for which the at least two selected genetic         changes are designed is the same as the at least one microbial         background strain for which data representing measured         responsive performance was obtained.     -   61. A system for applying epistatic effects in the iterative         improvement of candidate microbial strains, the system         comprising:         -   one or more processors; and         -   one or more memories operatively coupled to at least one of             the one or more processors and having instructions stored             thereon that, when executed by at least one of the one or             more processors, cause the system to:         -   obtain data representing measured performance in response to             corresponding genetic changes made to at least one microbial             background strain;         -   obtain a selection of at least two genetic changes based at             least in part upon a degree of dissimilarity between the             corresponding responsive performance measures of the at             least two genetic changes,         -   wherein the degree of dissimilarity relates to the degree to             which the at least two genetic changes affect their             corresponding responsive performance measures through             different biological pathways; and         -   design genetic changes to a microbial background strain that             include the selected genetic changes.     -   62. The system of embodiment 61, wherein the microbial         background strain for which the at least two selected genetic         changes are designed is the same as the at least one microbial         background strain for which data representing measured         responsive performance was obtained.     -   63. One or more non-transitory computer readable media storing         instructions for applying epistatic effects in the iterative         improvement of candidate microbial strains, wherein the         instructions, when executed by one or more computing devices,         cause at least one of the one or more computing devices to:         -   obtain data representing measured performance in response to             corresponding genetic changes made to at least one microbial             background strain;         -   obtain a selection of at least two genetic changes based at             least in part upon a degree of dissimilarity between the             corresponding responsive performance measures of the at             least two genetic changes,         -   wherein the degree of dissimilarity relates to the degree to             which the at least two genetic changes affect their             corresponding responsive performance measures through             different biological pathways; and         -   design genetic changes to a microbial background strain that             include the selected genetic changes.     -   64. The computer readable media of embodiment 63, wherein the         microbial background strain for which the at least two selected         genetic changes are designed is the same as the at least one         microbial background strain for which data representing measured         responsive performance was obtained.

INCORPORATION BY REFERENCE

All references, articles, publications, patents, patent publications, and patent applications cited herein are incorporated by reference in their entireties for all purposes. However, mention of any reference, article, publication, patent, patent publication, and patent application cited herein is not, and should not be taken as an acknowledgment or any form of suggestion that they constitute valid prior art or form part of the common general knowledge in any country in the world. 

What is claimed is:
 1. A functionally agnostic method for rehabilitating and improving the phenotypic performance of a production microbial strain, which does not require prior knowledge regarding the underlying function of a given genetic variation, the method comprising the steps of: a. providing a parental lineage microbial strain and a production microbial strain derived therefrom, wherein the production microbial strain comprises a plurality of identified genetic variations selected from single nucleotide polymorphisms, DNA insertions, and DNA deletions, not present in the parental lineage microbial strain; b. perturbing the genome of the parental lineage microbial strain to add one or more of the identified genetic variations present in the production microbial strain, or perturbing the genome of the production microbial strain to remove one or more of the identified genetic variations not present in the parental lineage microbial strain, to create an initial library of microbial strains, wherein each strain in the initial library comprises a genetic variation from the plurality of identified genetic variations between the parental lineage microbial strain and the production microbial strain, and wherein at least one of the strains of the initial library comprises a genetic variation that does not have a known enzymatic or regulatory function; c. screening and selecting individual strains of the initial library for phenotypic performance improvements over a reference microbial strain, thereby identifying genetic variations that confer phenotypic performance improvements; d. providing a subsequent plurality of microbes that each comprise a combination of genetic variations from the genetic variations present in at least two individual microbial strains screened in the preceding step, to thereby create a subsequent library of microbial strains; e. screening and selecting individual strains of the subsequent library for phenotypic performance improvements over the reference microbial strain, thereby identifying combinations of genetic variation that confer additional phenotypic performance improvements; and f. repeating steps d)-e) one or more times, in a linear or non-linear fashion, until a microbial strain exhibits a desired level of improved phenotypic performance compared to the phenotypic performance of the production microbial strain, wherein each subsequent iteration creates a new library of microbial strains, where each strain in the new library comprises genetic variations that are a combination of genetic variations selected from amongst at least two individual microbial strains of a preceding library; and wherein the method enables analyzing genome-wide combinatorial effects of genetic variations across multiple disparate genomic regions, including uncharacterized genes and/or genes of no known function.
 2. The method according to claim 1, wherein the initial library is a subset of a full combinatorial library comprising a subset of the identified genetic variations between the parental lineage microbial strain and the production microbial strain.
 3. The method according to claim 1, wherein the subsequent library is a subset of a full combinatorial library of the initial library.
 4. The method according to claim 1, wherein the subsequent library is a subset of a full combinatorial library of a preceding library.
 5. The method according to claim 1, wherein perturbing the genome comprises utilizing at least one method selected from the group consisting of: random mutagenesis, targeted sequence insertions, targeted sequence deletions, targeted sequence replacements, and combinations thereof.
 6. The method according to claim 1, wherein steps d)-e) are repeated until the phenotypic performance of a microbial strain of a subsequent library exhibits at least a 10% increase in a measured phenotypic variable compared to the phenotypic performance of the production microbial strain.
 7. The method according to claim 1, wherein steps d)-e) are repeated until the phenotypic performance of a microbial strain of a subsequent library exhibits at least a one-fold increase in a measured phenotypic variable compared to the phenotypic performance of the production microbial strain.
 8. The method according to claim 1, wherein the improved phenotypic performance of step f) is selected from the group consisting of: volumetric productivity of a product of interest, specific productivity of a product of interest, yield of a product of interest, titer of a product of interest, and combinations thereof.
 9. The method according to claim 1, wherein the improved phenotypic performance of step f) is: increased or more efficient production of a product of interest, said product of interest selected from the group consisting of: a small molecule, enzyme, protein, peptide, amino acid, organic acid, synthetic compound, fuel, alcohol, primary extracellular metabolite, secondary extracellular metabolite, intracellular component molecule, and combinations thereof.
 10. The method according to claim 1, wherein said production microbial strain is a prokaryote.
 11. The method according to claim 1, wherein said production microbial strain is from a genus selected from the group consisting of: Agrobacterium, Alicyclobacillus, Anabaena, Anacystis, Acinetobacter, Acidothermus, Arthrobacter, Azobacter, Bacillus, Bifidobacterium, Brevibacterium, Butyrivibrio, Buchnera, Campestris, Camplyobacter, Clostridium, Corynebacterium, Chromatium, Coprococcus, Escherichia, Enterococcus, Enterobacter, Erwinia, Fusobacterium, Faecalibacterium, Francisella, Flavobacterium, Geobacillus, Haemophilus, Helicobacter, Klebsiella, Lactobacillus, Lactococcus, Ilyobacter, Micrococcus, Microbacterium, Mesorhizobium, Methylobacterium, Methylobacterium, Mycobacterium, Neisseria, Pantoea, Pseudomonas, Prochlorococcus, Rhodobacter, Rhodopseudomonas, Roseburia, Rhodospirillum, Rhodococcus, Scenedesmus, Streptomyces, Streptococcus, Synecoccus, Saccharomonospora, Saccharopolyspora, Staphylococcus, Serratia, Salmonella, Shigella, Thermoanaerobacterium, Tropheryma, Tularensis, Temecula, Thermosynechococcus, Thermococcus, Ureaplasma, Xanthomonas, Xylella, Yersinia, and Zymomonas.
 12. The method according to claim 1, wherein said production microbial strain is Corynebacterium glutamicum.
 13. The method according to claim 1, wherein said production microbial strain is a eukaryote.
 14. The method according to claim 1, wherein said production microbial strain is from a genus selected from the group consisting of: Achlya, Acremonium, Aspergillus, Aureobasidium, Bjerkandera, Ceriporiopsis, Cephalosporium, Chrysosporium, Cochliobolus, Corynascus, Cryphonectria, Cryptococcus, Coprinus, Coriolus, Diplodia, Endothis, Fusarium, Gibberella, Gliocladium, Humicola, Hypocrea, Myceliophthora, Mucor, Neurospora, Penicillium, Podospora, Phlebia, Piromyces, Pyricularia, Rhizomucor, Rhizopus, Schizophyllum, Scytalidium, Sporotrichum, Talaromyces, Thermoascus, Thielavia, Tramates, Tolypocladium, Trichoderma, Verticillium, and Volvariella.
 15. The method according to claim 1, wherein said production microbial strain is Aspergillus niger. 